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Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -23,9 +23,9 @@\n     * available_moltypes_\u00bb\n [q                   ]\n \n ****** available_codes\u00c2\u00b6 ******\n   available_codes()\u00c2\u00b6\n       returns Table listing the available genetic codes\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.available_models.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.available_models.html", "unified_diff": "@@ -138,14 +138,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -23,9 +23,9 @@\n     * available_apps_\u00bb\n [q                   ]\n \n ****** available_models\u00c2\u00b6 ******\n   available_models(model_types=None)\u00c2\u00b6\n       returns Table listing the pre-defined substitution models\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.available_moltypes.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.available_moltypes.html", "unified_diff": "@@ -138,14 +138,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -23,9 +23,9 @@\n     * available_models_\u00bb\n [q                   ]\n \n ****** available_moltypes\u00c2\u00b6 ******\n   available_moltypes()\u00c2\u00b6\n       returns Table listing the available moltypes\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.get_code.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.get_code.html", "unified_diff": "@@ -144,14 +144,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -26,9 +26,9 @@\n ****** get_code\u00c2\u00b6 ******\n   get_code(code_id=1)\u00c2\u00b6\n       returns the genetic code\n         Parameters:\n             code_id \u00e2\u0080\u0093 genetic code identifier, name, number or string\n             (number), defaults to standard genetic code\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.get_model.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.get_model.html", "unified_diff": "@@ -150,14 +150,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -31,9 +31,9 @@\n                 * optimise_motif_probs (bool) \u00e2\u0080\u0093 Treat like other free\n                   parameters.\n                 * recode_gaps (bool) \u00e2\u0080\u0093 Whether gaps in an alignment should be\n                   treated as an ambiguous state instead.\n       Notes\n       See available_models() for the full list.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.get_moltype.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.get_moltype.html", "unified_diff": "@@ -138,14 +138,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -23,9 +23,9 @@\n     * get_model_\u00bb\n [q                   ]\n \n ****** get_moltype\u00c2\u00b6 ******\n   get_moltype(name)\u00c2\u00b6\n       returns the moltype with the matching name attribute\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_aligned_seqs.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_aligned_seqs.html", "unified_diff": "@@ -153,14 +153,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -37,9 +37,9 @@\n                   otherwise an annotatable Alignment\n                 * label_to_name \u00e2\u0080\u0093 function for converting original name into\n                   another name.\n                 * parser_kw (dict) \u00e2\u0080\u0093 optional arguments for the parser\n         Return type:\n             ArrayAlignment or Alignment instance\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_delimited.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_delimited.html", "unified_diff": "@@ -155,14 +155,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -38,9 +38,9 @@\n                   legend\n                 * limit (int) \u00e2\u0080\u0093 maximum number of lines to read from the file\n         Return type:\n             header, rows, title, legend\n       Notes\n       All row values remain as strings.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_seq.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_seq.html", "unified_diff": "@@ -159,14 +159,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -41,9 +41,9 @@\n                 * **kw \u00e2\u0080\u0093 other keyword arguments passed to SequenceCollection\n       Notes\n       Returns one sequence from a file. Use load_aligned_seqs or\n       load_unaligned_seqs to get a collection.\n         Return type:\n             Sequence\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_table.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_table.html", "unified_diff": "@@ -165,14 +165,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -52,9 +52,9 @@\n                   that will handle the formatting.\n                 * limit \u00e2\u0080\u0093 exits after this many lines. Only applied for non\n                   pickled data file types.\n                 * format \u00e2\u0080\u0093 output format when using str(Table)\n                 * skip_inconsistent \u00e2\u0080\u0093 skips rows that have different length\n                   to header row\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_tree.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_tree.html", "unified_diff": "@@ -158,14 +158,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -35,9 +35,9 @@\n                   in all names read, i.e. \u00e2\u0080\u009csp_name\u00e2\u0080\u009d becomes \u00e2\u0080\u009csp name\u00e2\u0080\u009d.\n       Notes\n       Underscore unmunging is turned off by default, although it is part of the\n       Newick format. Only the cogent3 json and xml tree formats are supported.\n         Return type:\n             PhyloNode\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_unaligned_seqs.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_unaligned_seqs.html", "unified_diff": "@@ -154,14 +154,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -37,9 +37,9 @@\n                   another name.\n                 * parser_kw (dict) \u00e2\u0080\u0093 optional arguments for the parser\n                 * info \u00e2\u0080\u0093 a dict from which to make an info object\n                 * **kw \u00e2\u0080\u0093 other keyword arguments passed to SequenceCollection\n         Return type:\n             SequenceCollection\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_aligned_seqs.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_aligned_seqs.html", "unified_diff": "@@ -152,14 +152,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -36,9 +36,9 @@\n                 * label_to_name \u00e2\u0080\u0093 function for converting original name into\n                   another name.\n                 * info \u00e2\u0080\u0093 a dict from which to make an info object\n                 * source \u00e2\u0080\u0093 origins of this data, defaults to \u00e2\u0080\u0098unknown\u00e2\u0080\u0099.\n                   Converted to a string and added to info[\u00e2\u0080\u009csource\u00e2\u0080\u009d].\n                 * **kw \u00e2\u0080\u0093 other keyword arguments passed to alignment class\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_seq.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_seq.html", "unified_diff": "@@ -149,14 +149,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -28,9 +28,9 @@\n         Parameters:\n                 * seq (str) \u00e2\u0080\u0093 raw string to be converted to sequence object\n                 * name (str) \u00e2\u0080\u0093 sequence name\n                 * moltype \u00e2\u0080\u0093 name of a moltype or moltype instance\n         Return type:\n             returns a sequence object\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_table.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_table.html", "unified_diff": "@@ -162,14 +162,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -46,9 +46,9 @@\n                 * column_templates \u00e2\u0080\u0093 dict of column headings or a function\n                   that will handle the formatting.\n                 * limit \u00e2\u0080\u0093 exits after this many lines. Only applied for non\n                   pickled data file types.\n                 * data_frame \u00e2\u0080\u0093 a pandas DataFrame, supersedes header/rows\n                 * format \u00e2\u0080\u0093 output format when using str(Table)\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_tree.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_tree.html", "unified_diff": "@@ -158,14 +158,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -37,9 +37,9 @@\n                   in all names read, i.e. \u00e2\u0080\u009csp_name\u00e2\u0080\u009d becomes \u00e2\u0080\u009csp name\u00e2\u0080\u009d\n       Notes\n       Underscore unmunging is turned off by default, although it is part of the\n       Newick format.\n         Return type:\n             PhyloNode\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_unaligned_seqs.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_unaligned_seqs.html", "unified_diff": "@@ -151,14 +151,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -34,9 +34,9 @@\n                 * label_to_name \u00e2\u0080\u0093 function for converting original name into\n                   another name.\n                 * info \u00e2\u0080\u0093 a dict from which to make an info object\n                 * source \u00e2\u0080\u0093 origins of this data, defaults to \u00e2\u0080\u0098unknown\u00e2\u0080\u0099.\n                   Converted to a string and added to info[\u00e2\u0080\u009csource\u00e2\u0080\u009d].\n                 * **kw \u00e2\u0080\u0093 other keyword arguments passed to SequenceCollection\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/alignment/alignment.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/alignment/alignment.html", "unified_diff": "@@ -142,14 +142,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -25,9 +25,9 @@\n ****** alignment\u00c2\u00b6 ******\n SequenceCollection(data            Container for unaligned sequences\n [,\u00c2\u00a0names,\u00c2\u00a0alphabet,\u00c2\u00a0...])\n Alignment(*args,\u00c2\u00a0**kwargs)      An annotatable alignment class\n ArrayAlignment(*args,\u00c2\u00a0**kwargs) Holds a dense array representing a multiple\n                                    sequence alignment.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/alignment/classes/cogent3.core.alignment.Alignment.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/alignment/classes/cogent3.core.alignment.Alignment.html", "unified_diff": "@@ -1544,14 +1544,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -877,9 +877,9 @@\n               Parameters:\n                       * filename \u00e2\u0080\u0093 name of the sequence file\n                       * format \u00e2\u0080\u0093 format of the sequence file\n             Notes\n             If format is None, will attempt to infer format from the filename\n             suffix.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/alignment/classes/cogent3.core.alignment.ArrayAlignment.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/alignment/classes/cogent3.core.alignment.ArrayAlignment.html", "unified_diff": "@@ -1433,14 +1433,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -881,9 +881,9 @@\n               Parameters:\n                       * filename \u00e2\u0080\u0093 name of the sequence file\n                       * format \u00e2\u0080\u0093 format of the sequence file\n             Notes\n             If format is None, will attempt to infer format from the filename\n             suffix.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/alignment/classes/cogent3.core.alignment.SequenceCollection.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/alignment/classes/cogent3.core.alignment.SequenceCollection.html", "unified_diff": "@@ -767,14 +767,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -431,9 +431,9 @@\n               Parameters:\n                       * filename \u00e2\u0080\u0093 name of the sequence file\n                       * format \u00e2\u0080\u0093 format of the sequence file\n             Notes\n             If format is None, will attempt to infer format from the filename\n             suffix.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/alphabet/alphabet.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/alphabet/alphabet.html", "unified_diff": "@@ -136,14 +136,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -22,9 +22,9 @@\n     * Alphabet_\u00bb\n [q                   ]\n \n ****** alphabet\u00c2\u00b6 ******\n Alphabet(motifset[,\u00c2\u00a0gap,\u00c2\u00a0moltypAn ordered set of fixed-length strings,\n                                      e.g. the 61 sense codons.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/alphabet/classes/cogent3.core.alphabet.Alphabet.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/alphabet/classes/cogent3.core.alphabet.Alphabet.html", "unified_diff": "@@ -394,14 +394,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -173,9 +173,9 @@\n         to_json()\u00c2\u00b6\n             returns result of json formatted string\n         to_rich_dict(for_pickle=False)\u00c2\u00b6\n         with_gap_motif()\u00c2\u00b6\n             Returns an Alphabet object resembling self but including the gap.\n             Always returns the same object.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/apps/composable.define_app.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/apps/composable.define_app.html", "unified_diff": "@@ -234,14 +234,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -106,9 +106,9 @@\n       ...                                 moltype=moltype\n       ...                                 )\n       omit_seqs is now an app, allowing creating different variants which can\n       be composed as per ones defined via a class.\n       >>> omit_bad = omit_seqs(quantile=0.95)\n       and omit_bad is an instance of that app.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode.html", "unified_diff": "@@ -250,14 +250,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -90,9 +90,9 @@\n                         implement frames)\n               Returns:\n                       * String containing amino acid sequence. Translates the\n                         entire sequence.\n                       * It is the caller\u00e2\u0080\u0099s responsibility to find open\n                         reading frames.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/genetic_code/genetic_code.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/genetic_code/genetic_code.html", "unified_diff": "@@ -136,14 +136,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -22,9 +22,9 @@\n     * GeneticCode_\u00bb\n [q                   ]\n \n ****** genetic_code\u00c2\u00b6 ******\n GeneticCode(code_sequence   Holds codon to amino acid mapping, and vice\n [,\u00c2\u00a0ID,\u00c2\u00a0name,\u00c2\u00a0...]) versa.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/index.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/index.html", "unified_diff": "@@ -227,14 +227,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -74,9 +74,9 @@\n     * table\n     * tree\n \n ***** Defining Composable Apps\u00c2\u00b6 *****\n     * define_app\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/moltype/classes/cogent3.core.moltype.MolType.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/moltype/classes/cogent3.core.moltype.MolType.html", "unified_diff": "@@ -513,14 +513,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -225,9 +225,9 @@\n             is probably useful to have in parallel with the validation routines\n             that check specifically whether the sequence has gaps, degenerate\n             symbols, etc., or that explicitly take an alphabet as input.\n         what_ambiguity(motifs)\u00c2\u00b6\n             The code that represents all of \u00e2\u0080\u0098motifs\u00e2\u0080\u0099, and minimal others.\n             Does this duplicate DegenerateFromSequence directly?\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/moltype/moltype.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/moltype/moltype.html", "unified_diff": "@@ -136,14 +136,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -23,9 +23,9 @@\n [q                   ]\n \n ****** moltype\u00c2\u00b6 ******\n MolType(motifset                         MolType: Handles operations that\n [,\u00c2\u00a0gap,\u00c2\u00a0missing,\u00c2\u00a0gaps,\u00c2\u00a0...]) depend on the sequence type (e.g.\n                                          DNA).\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/sequence/classes/cogent3.core.sequence.DnaSequence.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/sequence/classes/cogent3.core.sequence.DnaSequence.html", "unified_diff": "@@ -1014,14 +1014,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -492,9 +492,9 @@\n                       * shadow \u00e2\u0080\u0093 whether to mask the annotated regions, or\n                         everything but the annotated regions\n                       * extend_query (boolean) \u00e2\u0080\u0093 queries sub-annotations if\n                         True\n         with_termini_unknown()\u00c2\u00b6\n             Returns copy of sequence with terminal gaps remapped as missing.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/sequence/classes/cogent3.core.sequence.ProteinSequence.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/sequence/classes/cogent3.core.sequence.ProteinSequence.html", "unified_diff": "@@ -916,14 +916,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -446,9 +446,9 @@\n                       * shadow \u00e2\u0080\u0093 whether to mask the annotated regions, or\n                         everything but the annotated regions\n                       * extend_query (boolean) \u00e2\u0080\u0093 queries sub-annotations if\n                         True\n         with_termini_unknown()\u00c2\u00b6\n             Returns copy of sequence with terminal gaps remapped as missing.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/sequence/classes/cogent3.core.sequence.RnaSequence.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/sequence/classes/cogent3.core.sequence.RnaSequence.html", "unified_diff": "@@ -1014,14 +1014,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -492,9 +492,9 @@\n                       * shadow \u00e2\u0080\u0093 whether to mask the annotated regions, or\n                         everything but the annotated regions\n                       * extend_query (boolean) \u00e2\u0080\u0093 queries sub-annotations if\n                         True\n         with_termini_unknown()\u00c2\u00b6\n             Returns copy of sequence with terminal gaps remapped as missing.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/sequence/sequence.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/sequence/sequence.html", "unified_diff": "@@ -142,14 +142,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -26,9 +26,9 @@\n DnaSequence(                               Holds the standard DNA sequence.\n [seq,\u00c2\u00a0name,\u00c2\u00a0info,\u00c2\u00a0check,\u00c2\u00a0...])\n RnaSequence(                               Holds the standard RNA sequence.\n [seq,\u00c2\u00a0name,\u00c2\u00a0info,\u00c2\u00a0check,\u00c2\u00a0...])\n ProteinSequence(                           Holds the standard Protein sequence.\n [seq,\u00c2\u00a0name,\u00c2\u00a0info,\u00c2\u00a0check,\u00c2\u00a0...])\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.parse.table.FilteringParser.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.parse.table.FilteringParser.html", "unified_diff": "@@ -138,14 +138,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -25,9 +25,9 @@\n \n ****** FilteringParser\u00c2\u00b6 ******\n   classFilteringParser(row_condition=None, negate=False, with_header=True,\n   columns=None, sep=',', limit=None)\u00c2\u00b6\n       A parser for a delimited tabular file that returns records matching a\n       condition.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.util.table.Columns.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.util.table.Columns.html", "unified_diff": "@@ -261,14 +261,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -75,9 +75,9 @@\n         F.\u00c2\u00b6\n             If E present and has a .keys() method, does: for k in E: D[k] = E\n             [k] If E present and lacks .keys() method, does: for (k, v) in E: D\n             [k] = v In either case, this is followed by: for k, v in F.items():\n             D[k] = v\n         values() &#x2192; an object providing a view on D's values\u00c2\u00b6\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.util.table.Table.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.util.table.Table.html", "unified_diff": "@@ -773,14 +773,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -379,9 +379,9 @@\n                       * compress \u00e2\u0080\u0093 if True, gzips the file and appends .gz to\n                         the filename (if not already added).\n             Notes\n             If a format is not specified, it attempts to use a filename suffix.\n             Unformatted numerical values are written to file in order to\n             preserve numerical accuracy.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/table/table.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/table/table.html", "unified_diff": "@@ -148,14 +148,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -24,9 +24,9 @@\n \n ****** table\u00c2\u00b6 ******\n Table([header,\u00c2\u00a0data,\u00c2\u00a0index_name,\u00c2\u00a0title,\u00c2Tabular data.\n Columns()                                         Collection of columns.\n FilteringParser(                    A parser for a delimited tabular file that\n [row_condition,\u00c2\u00a0negate,\u00c2\u00a0...]) returns records matching a condition.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/tree/classes/cogent3.core.tree.PhyloNode.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/tree/classes/cogent3.core.tree.PhyloNode.html", "unified_diff": "@@ -284,15 +284,15 @@\n <p>Note: names present in only one of the two trees will count as\n mismatches: if you don\u2019t want this behavior, strip out the non-matching\n tips first.</p>\n </dd></dl>\n \n <dl class=\"py method\">\n <dt class=\"sig sig-object py\" id=\"cogent3.core.tree.PhyloNode.compare_by_tip_distances\">\n-<span class=\"sig-name descname\"><span class=\"pre\">compare_by_tip_distances</span></span><span class=\"sig-paren\">(</span><em class=\"sig-param\"><span class=\"n\"><span class=\"pre\">other</span></span></em>, <em class=\"sig-param\"><span class=\"n\"><span class=\"pre\">sample=None</span></span></em>, <em class=\"sig-param\"><span class=\"n\"><span class=\"pre\">dist_f=&lt;function</span> <span class=\"pre\">distance_from_r&gt;</span></span></em>, <em class=\"sig-param\"><span class=\"n\"><span class=\"pre\">shuffle_f=&lt;bound</span> <span class=\"pre\">method</span> <span class=\"pre\">Random.shuffle</span> <span class=\"pre\">of</span> <span class=\"pre\">&lt;random.Random</span> <span class=\"pre\">object</span> <span class=\"pre\">at</span> <span class=\"pre\">0x1421ab0&gt;&gt;</span></span></em><span class=\"sig-paren\">)</span><a class=\"headerlink\" href=\"#cogent3.core.tree.PhyloNode.compare_by_tip_distances\" title=\"Link to this definition\">\u00b6</a></dt>\n+<span class=\"sig-name descname\"><span class=\"pre\">compare_by_tip_distances</span></span><span class=\"sig-paren\">(</span><em class=\"sig-param\"><span class=\"n\"><span class=\"pre\">other</span></span></em>, <em class=\"sig-param\"><span class=\"n\"><span class=\"pre\">sample=None</span></span></em>, <em class=\"sig-param\"><span class=\"n\"><span class=\"pre\">dist_f=&lt;function</span> <span class=\"pre\">distance_from_r&gt;</span></span></em>, <em class=\"sig-param\"><span class=\"n\"><span class=\"pre\">shuffle_f=&lt;bound</span> <span class=\"pre\">method</span> <span class=\"pre\">Random.shuffle</span> <span class=\"pre\">of</span> <span class=\"pre\">&lt;random.Random</span> <span class=\"pre\">object</span> <span class=\"pre\">at</span> <span class=\"pre\">0xffbcb0&gt;&gt;</span></span></em><span class=\"sig-paren\">)</span><a class=\"headerlink\" href=\"#cogent3.core.tree.PhyloNode.compare_by_tip_distances\" title=\"Link to this definition\">\u00b6</a></dt>\n <dd><p>Compares self to other using tip-to-tip distance matrices.</p>\n <p>Value returned is dist_f(m1, m2) for the two matrices. Default is\n to use the Pearson correlation coefficient, with +1 giving a distance\n of 0 and -1 giving a distance of +1 (the madimum possible value).\n Depending on the application, you might instead want to use\n distance_from_r_squared, which counts correlations of both +1 and -1\n as identical (0 distance).</p>\n@@ -999,14 +999,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -144,15 +144,15 @@\n             differ.\n             Other is expected to be a tree object compatible with PhyloNode.\n             Note: names present in only one of the two trees will count as\n             mismatches: if you don\u00e2\u0080\u0099t want this behavior, strip out the non-\n             matching tips first.\n         compare_by_tip_distances(other, sample=None, dist_f=<function\n         distance_from_r>, shuffle_f=<bound method Random.shuffle of\n-        <random.Random object at 0x1421ab0>>)\u00c2\u00b6\n+        <random.Random object at 0xffbcb0>>)\u00c2\u00b6\n             Compares self to other using tip-to-tip distance matrices.\n             Value returned is dist_f(m1, m2) for the two matrices. Default is\n             to use the Pearson correlation coefficient, with +1 giving a\n             distance of 0 and -1 giving a distance of +1 (the madimum possible\n             value). Depending on the application, you might instead want to use\n             distance_from_r_squared, which counts correlations of both +1 and -\n             1 as identical (0 distance).\n@@ -502,9 +502,9 @@\n                       * format \u00e2\u0080\u0093 default is newick, xml and json are\n                         alternate. Argument overrides the filename suffix. All\n                         attributes are saved in the xml format. Value overrides\n                         the file name suffix.\n             Notes\n             Only the cogent3 json and xml tree formats are supported.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/tree/tree.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/tree/tree.html", "unified_diff": "@@ -136,14 +136,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -21,9 +21,9 @@\n     * \u00ab_FilteringParser\n     * PhyloNode_\u00bb\n [q                   ]\n \n ****** tree\u00c2\u00b6 ******\n PhyloNode(*args,\u00c2\u00a0**kwargs)\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/align-codon.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/align-codon.html", "unified_diff": "@@ -180,14 +180,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -65,9 +65,9 @@\n \n ***** Alignment settings and file provenance are recorded in the info\n attribute\u00c2\u00b6 *****\n The parameters used to construct the alignment, including the guide tree and\n substitution model, are record in the alignment info attribute.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/align-nucleotide.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/align-nucleotide.html", "unified_diff": "@@ -167,14 +167,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -52,9 +52,9 @@\n You can use any cogent3 nucleotide substitution model. For a list of all\n available, see cogent3.available_models().\n \n ***** Alignment settings and file provenance are recorded in the info\n attribute\u00c2\u00b6 *****\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/align-protein.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/align-protein.html", "unified_diff": "@@ -150,14 +150,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -40,9 +40,9 @@\n An estimated guide tree has its branch lengths scaled so they are consistent\n with usage in a codon model.\n \n ***** Alignment settings and file provenance are recorded in the info\n attribute\u00c2\u00b6 *****\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app-get.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app-get.html", "unified_diff": "@@ -130,14 +130,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -24,9 +24,9 @@\n \n ****** Getting an app\u00c2\u00b6 ******\n The get_app() function is a top-level import. It allows you to create an app\n instance by passing the name of the app you want as a string along with the\n values for any positional or keyword arguments. (See Getting_help_on_an_app.)\n Below, I create an omit_degenerates app for a DNA moltype.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app-help.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app-help.html", "unified_diff": "@@ -138,14 +138,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -33,9 +33,9 @@\n       using get_app() (Getting_an_app). It includes the positional and keyword\n       arguments for the app.\n    3. \u00e2\u0080\u009cParameters\u00e2\u0080\u009d lists the documentation describing the arguments.\n    4. \u00e2\u0080\u009cInput type\u00e2\u0080\u009d states what data types are acceptable as input to the\n       app.\n    5. \u00e2\u0080\u009cOutput type\u00e2\u0080\u009d states what data type will be generated by the app.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app-overview.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app-overview.html", "unified_diff": "@@ -246,14 +246,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -119,9 +119,9 @@\n Parallel_computations for more details plus how to take advantage of multiple\n machines using MPI.)\n \n **** All of the above\u00c2\u00b6 ****\n process.apply_to(dstore, parallel=True, show_progress=True)\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/available-apps.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/available-apps.html", "unified_diff": "@@ -130,14 +130,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -24,9 +24,9 @@\n \n ****** Displaying installed apps\u00c2\u00b6 ******\n Apps perform functions ranging from multiple sequence alignment (e.g.\n progressive_align), to excluding alignment columns containing non-nucleotide\n characters (e.g. omit_degenerates) to performing maximum-likelihood\n evolutionary analyses (e.g. model).\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/dstore.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/dstore.html", "unified_diff": "@@ -172,14 +172,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -68,9 +68,9 @@\n data store. This includes useful information regarding the run conditions that\n produced the contents of the data store.\n Log files can be accessed vial a special attribute.\n Each element in that list is a DataMember which you can use to get the data\n contents.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/evo-ancestral-states.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/evo-ancestral-states.html", "unified_diff": "@@ -139,14 +139,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -34,9 +34,9 @@\n position.\n If not included in the newick tree file, the internal node names are\n automatically generated open loading. You can establish what those are by\n interrogating the tree bound to the likelihood function object. (If you move\n your mouse cursor over the nodes, their names will appear as hover text.)\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/evo-dt-nuc-model.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/evo-dt-nuc-model.html", "unified_diff": "@@ -147,14 +147,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -38,9 +38,9 @@\n \n ***** Getting parameter estimates\u00c2\u00b6 *****\n For a discrete-time model, aside from the root motif probabilities, everything\n is edge specific. But note that the tabular_result has different keys from the\n continuous-time case, as demonstrated below.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/evo-extract-model-stats.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/evo-extract-model-stats.html", "unified_diff": "@@ -157,14 +157,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -45,9 +45,9 @@\n ***** Global parameters\u00c2\u00b6 *****\n These are the elements of the rate matrix.\n \n ***** Motif parameters\u00c2\u00b6 *****\n These are estimates of the nucleotide probabilities in the unobserved ancestor.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/evo-hypothesis.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/evo-hypothesis.html", "unified_diff": "@@ -166,14 +166,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -49,9 +49,9 @@\n from cogent3 import get_app, open_data_store\n \n output = open_data_store(\"path/to/myresults.sqlitedb\", mode=\"w\")\n writer = get_app(\"write_db\", data_store=output)\n writer(result)\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/evo-model-timehet.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/evo-model-timehet.html", "unified_diff": "@@ -141,14 +141,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -40,9 +40,9 @@\n assign to the time_het argument as follows.\n The outcome of this setting to model is that the black edges will share one\n rate matrix, the red edges another. We fit the model to the data.\n Examining the fitted likelihood function, the rate parameters differ between\n the edge sets.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/evo-model-with-tree.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/evo-model-with-tree.html", "unified_diff": "@@ -149,14 +149,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -37,9 +37,9 @@\n In the above, no value is shown for unique_Q. This can happen because of\n numerical precision issues.\n Note\n in the display of the lf below, the \u00e2\u0080\u009clength\u00e2\u0080\u009d parameter is not the ENS. It\n is, instead, just a scalar.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/evo-model.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/evo-model.html", "unified_diff": "@@ -153,14 +153,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -60,9 +60,9 @@\n from the fits to the individual positions. The DLC and unique_Q are also a\n summary across all models. These only achieve the value True when all matrices,\n from all models, satisfy the condition.\n We get access to the likelihood functions of the individual positions via the\n indicated dict keys.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/evo-natsel_neutral.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/evo-natsel_neutral.html", "unified_diff": "@@ -135,14 +135,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -27,9 +27,9 @@\n selection that has operated on a gene.\n Noting that \u00cf\u0089 (omega) is the ratio of nonsynonymous substitutions to\n synonymous substitutions, \u00cf\u0089=1 is indicative a gene is evolving neutrally.\n Warning\n I\u00e2\u0080\u0099m setting optimise_motif_probs=False to speed up execution of the examples,\n not because it\u00e2\u0080\u0099s a good idea!\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/evo-natsel_sitehet.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/evo-natsel_sitehet.html", "unified_diff": "@@ -140,14 +140,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -32,9 +32,9 @@\n of interest relating to these are the bprobs (the maximum likelihood estimate\n of the frequency of the site-class) and the corresponding value of omega.\n ***** Getting the individual site posterior probabilities\u00c2\u00b6 *****\n I\u00e2\u0080\u0099m just displaying the posterior-probabilities from the first 20 positions\n only.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/evo-natsel_timehet.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/evo-natsel_timehet.html", "unified_diff": "@@ -134,14 +134,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -26,9 +26,9 @@\n We employ codon models to test whether the mode of natural selection affecting\n human and chimpanzee lineages is distinctive. This is done by specifying the\n edges of interest (Yang_1998).\n Warning\n I\u00e2\u0080\u0099m setting optimise_motif_probs=False to speed up execution of the examples,\n not because it\u00e2\u0080\u0099s a good idea!\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/evo-natsel_zhang.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/evo-natsel_zhang.html", "unified_diff": "@@ -145,14 +145,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -38,9 +38,9 @@\n Our implementation is not as parametrically succinct as that of Zhang et al, we\n have 1 additional bin probability.\n ***** Getting the posterior probabilities of site-class membership\u00c2\u00b6 *****\n \n ***** Getting all the statistics in tabular form\u00c2\u00b6 *****\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/evo-nstat-codon-model.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/evo-nstat-codon-model.html", "unified_diff": "@@ -139,14 +139,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -29,9 +29,9 @@\n We apply this to a sample alignment.\n The model is specified using it\u00e2\u0080\u0099s abbreviation.\n ***** We can obtain the tree with branch lengths as ENS\u00c2\u00b6 *****\n If this tree is written to newick (using the write() method), the lengths will\n now be ENS.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/evo-tr-codon-model.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/evo-tr-codon-model.html", "unified_diff": "@@ -137,14 +137,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -28,9 +28,9 @@\n ***** Using the conditional nucleotide form codon model\u00c2\u00b6 *****\n The CNFGTR model (Yap_et_al) is the most robust of the time-reversible codon\n models available (Kaehler_et_al). By default, this model does not optimise the\n codon frequencies but uses the average estimated from the alignment. We\n configure the model to optimise the root motif probabilities.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/evo-tr-nuc-model.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/evo-tr-nuc-model.html", "unified_diff": "@@ -137,14 +137,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -28,9 +28,9 @@\n ***** Using the GTR model\u00c2\u00b6 *****\n We specify the general time-reversible model (Lanave_et_al) by its\n abbreviation. By default, this model does not optimise the codon frequencies\n but uses the average estimated from the alignment. We configure the model to\n optimise the root motif probabilities.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/index.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/index.html", "unified_diff": "@@ -218,14 +218,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -89,9 +89,9 @@\n     * natsel_zhang_\u00e2\u0080\u0093_a_branch-site_test\n \n ***** Write your own Apps\u00c2\u00b6 *****\n You can write your own apps.\n     * Turn_your_functions_into_composable_apps\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/not-completed.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/not-completed.html", "unified_diff": "@@ -152,14 +152,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -44,9 +44,9 @@\n An ERROR type is returned if an exception is raised during the calculation. We\n trigger it in this case by trying to open a non-existent file.\n \n ***** Composed functions propagate NotCompleted results\u00c2\u00b6 *****\n and\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/user_function.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/user_function.html", "unified_diff": "@@ -159,14 +159,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -50,9 +50,9 @@\n json.\n \n ***** A user app with a different output type\u00c2\u00b6 *****\n In this example, we make a function that returns a DistanceMatrix from an\n alignment.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/DNA_and_RNA_sequences.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/DNA_and_RNA_sequences.html", "unified_diff": "@@ -224,14 +224,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -98,9 +98,9 @@\n **** Return a randomized version of the sequence\u00c2\u00b6 ****\n print rnaseq.shuffle()\n ACAACUGGCUCUGAUG\n \n **** Remove gaps from a sequence\u00c2\u00b6 ****\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/alignments.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/alignments.html", "unified_diff": "@@ -414,14 +414,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -320,9 +320,9 @@\n filter partial sequences from an alignment.\n Note that following this call to omit_gap_seqs, the 4th column of filtered_aln\n is 100% gaps. This is generally not desirable, so a call to omit_gap_seqs is\n frequently followed with a call to omit_gap_pos with no parameters \u00e2\u0080\u0093 this\n defaults to removing positions which are all gaps:\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/alphabet.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/alphabet.html", "unified_diff": "@@ -151,14 +151,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -37,9 +37,9 @@\n \n ***** Convert a sequence into integers\u00c2\u00b6 *****\n \n ***** Convert integers to a sequence\u00c2\u00b6 *****\n or\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/annotations.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/annotations.html", "unified_diff": "@@ -300,14 +300,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -175,9 +175,9 @@\n Sequence features can be accessed via a containing Alignment.\n \n ***** Annotation display on sequences\u00c2\u00b6 *****\n We can display annotations on sequences, writing to file.\n We first make a sequence and add some annotations.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/building_alignments.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/building_alignments.html", "unified_diff": "@@ -150,14 +150,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -45,9 +45,9 @@\n ***** Converting gaps from aa-seq alignment to nuc seq alignment\u00c2\u00b6 *****\n We load some unaligned DNA sequences and show their translation.\n We load an alignment of these protein sequences.\n We then obtain an alignment of the DNA sequences from the alignment of their\n translation.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/building_phylogenies.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/building_phylogenies.html", "unified_diff": "@@ -166,14 +166,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -59,9 +59,9 @@\n \n ***** By ML\u00c2\u00b6 *****\n We illustrate the phylogeny reconstruction using maximum-likelihood using the\n F81 substitution model. We use the advanced-stepwise addition algorithm to\n search tree space.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/calc_genetic_distance.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/calc_genetic_distance.html", "unified_diff": "@@ -153,14 +153,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -42,9 +42,9 @@\n The standard cogent3 likelihood function can also be used to estimate\n distances. Because these require numerical optimisation they can be\n significantly slower than the fast estimation approach above.\n The following will use the F81 nucleotide substitution model and perform\n numerical optimisation.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/evo_modelling.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/evo_modelling.html", "unified_diff": "@@ -323,14 +323,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -242,9 +242,9 @@\n maximum likelihood values. So using the set_param_rule method to provide good\n starting values can be very useful. As this can be difficult to do one easy way\n is to build simpler models that are nested within the one you\u00e2\u0080\u0099re interested\n in. Fitting those models and then relaxing constraints until you\u00e2\u0080\u0099re at the\n parameterisation of interest can markedly improve optimisation speed.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/genetic_code.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/genetic_code.html", "unified_diff": "@@ -179,14 +179,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -58,9 +58,9 @@\n ****** Translating a DNA sequence with a terminating stop codon\u00c2\u00b6 ******\n You can\u00e2\u0080\u0099t translate a sequence that contains a stop codon.\n ***** By removing the trailing stop codon first\u00c2\u00b6 *****\n \n ***** By slicing the DnaSequence first\u00c2\u00b6 *****\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/index.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/index.html", "unified_diff": "@@ -144,14 +144,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -29,9 +29,9 @@\n     * Tabular_data\n     * Building_alignments\n     * Genetic_distance_calculation\n     * Building_phylogenies\n     * Evolutionary_Analysis_Using_Likelihood\n     * Useful_Utilities\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/loading_sequences.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/loading_sequences.html", "unified_diff": "@@ -210,14 +210,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -94,9 +94,9 @@\n flexibly addressed using the LabelParser. By creating a custom label parser, we\n can decide which part we use as the sequence name. We show how to convert a\n field into something specific.\n RichLabel objects have an Info object as an attribute, allowing specific\n reference to all the specified label fields.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/loading_tabular.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/loading_tabular.html", "unified_diff": "@@ -238,14 +238,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -113,9 +113,9 @@\n \n ****** Create a table from a 2D dict\u00c2\u00b6 ******\n \n ****** Create a table that has complex python objects as elements\u00c2\u00b6 ******\n \n ****** Create an empty table\u00c2\u00b6 ******\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/manipulating_biological_data.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/manipulating_biological_data.html", "unified_diff": "@@ -179,14 +179,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -53,9 +53,9 @@\n     * Obtaining_the_codons_from_a_DnaSequence_object\n     * Translating_a_DNA_sequence_with_a_terminating_stop_codon\n \n ***** Trees\u00c2\u00b6 *****\n     * Trees\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/moltypes.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/moltypes.html", "unified_diff": "@@ -173,14 +173,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -61,9 +61,9 @@\n At present, constructing a custom MolType that overrides a builtin one affects\n the original (in this instance, the DnaSequence class). All subsequent calls to\n the original class in the running process that made the change are affected.\n The below code is resetting this attribute now to allow the rest of the\n documentation to be executed.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/protein_sequences.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/protein_sequences.html", "unified_diff": "@@ -144,14 +144,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -32,9 +32,9 @@\n ***** Converting a DNA sequence string to protein sequence string\u00c2\u00b6 *****\n Conversion to a ProteinSequence from a DnaSequence is shown in Translate_a\n DnaSequence_to_protein.\n \n ***** Loading protein sequences from a Phylip file\u00c2\u00b6 *****\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/simple_trees.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/simple_trees.html", "unified_diff": "@@ -309,14 +309,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -148,9 +148,9 @@\n Score ranges from 0 (minimum distance) to 1 (maximum distance). The default is\n to use Pearson\u00e2\u0080\u0099s correlation, in which case a score of 0 means that the\n Pearson\u00e2\u0080\u0099s correlation was perfectly good (1), and a score of 1 means that the\n Pearson\u00e2\u0080\u0099s correlation was perfectly bad (-1).\n Note: automatically strips out the names that don\u00e2\u0080\u0099t match.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/tables.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/tables.html", "unified_diff": "@@ -546,14 +546,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -375,9 +375,9 @@\n ***** Writing a latex formmated file\u00c2\u00b6 *****\n \n ***** Writing delimited formats\u00c2\u00b6 *****\n The delimiter can be specified explicitly using the sep argument or implicitly\n via the file name suffix.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/useful_utilities.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/useful_utilities.html", "unified_diff": "@@ -229,14 +229,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -125,9 +125,9 @@\n ConstrainedContainer which can be used to construct user-defined constrained\n objects. Cogent3 also provides ConstrainedString, ConstrainedList, and\n ConstrainedDict. These provided types fully cover the builtin types while\n staying integrated with the ConstrainedContainer.\n Here is a light example of the ConstrainedDict\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/what_codes.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/what_codes.html", "unified_diff": "@@ -139,14 +139,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -30,9 +30,9 @@\n We specify the genetic code, and that codons that are incomplete as they\n contain a gap, are converted to ?.\n ***** Getting a genetic code with get_code()\u00c2\u00b6 *****\n This function can be used directly to get a genetic code. We will get the code\n with ID 4.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/data_file_links.html", "source2": "./usr/share/doc/python-cogent-doc/html/data_file_links.html", "unified_diff": "@@ -149,14 +149,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -46,9 +46,9 @@\n tree-with-support.json\n F9-demo.fa\n BRCA1-demo.fasta\n tbp.jaspar\n stats.tsv\n CerebellumDukeDNaseSeq.pk\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-coevolution.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-coevolution.html", "unified_diff": "@@ -135,14 +135,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -31,9 +31,9 @@\n corresponding plot types \u00e2\u0080\u0093 a heatmap in this case.\n \n ***** Display coevolution scores as a Violin plot\u00c2\u00b6 *****\n \n ***** Display coevolution scores as a Boxplot\u00c2\u00b6 *****\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-dotplot-1.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-dotplot-1.html", "unified_diff": "@@ -142,14 +142,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -41,9 +41,9 @@\n Note\n clicking on an entry in the legend turns it off\n \n ***** Setting plot attributes\u00c2\u00b6 *****\n I\u00e2\u0080\u0099ll modify the title and figure width.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-dotplot-2.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-dotplot-2.html", "unified_diff": "@@ -132,14 +132,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -30,9 +30,9 @@\n canonical transcript, then the SequenceCollection was saved as json using\n cogent3.app.write_json.\n \n ***** Removing annotation tracks\u00c2\u00b6 *****\n Thus we could remove the left annotation track, for instance with\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-gaps-per-seq.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-gaps-per-seq.html", "unified_diff": "@@ -139,14 +139,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -38,9 +38,9 @@\n ***** Displaying unique gaps as a bar chart\u00c2\u00b6 *****\n \n ***** Displaying unique gaps as a violin plot\u00c2\u00b6 *****\n \n ***** Displaying unique gaps as a box plot\u00c2\u00b6 *****\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-info-plot.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-info-plot.html", "unified_diff": "@@ -131,14 +131,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -26,9 +26,9 @@\n at a position.\n ***** Illustrated with a simple example\u00c2\u00b6 *****\n \n ***** On a sample data set\u00c2\u00b6 *****\n Clicking on any of the legend items causes that to disappear from the plot.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-seqlogo.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-seqlogo.html", "unified_diff": "@@ -137,14 +137,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -34,9 +34,9 @@\n time to render. Note that we include gap characters in the display.\n \n ***** Sequence logo of protein alignment\u00c2\u00b6 *****\n No difference here except it uses the built-in colour scheme from the protein\n MolType.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/index.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/index.html", "unified_diff": "@@ -327,14 +327,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -79,9 +79,9 @@\n [thumbnail]\n  Radial_Dendrogram_Style\n [thumbnail]\n  Circular_Dendrogram_Style\n [thumbnail]\n  Angular_Dendrogram_Style\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-angular.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-angular.html", "unified_diff": "@@ -126,14 +126,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -21,9 +21,9 @@\n \n ****** Angular Dendrogram Style\u00c2\u00b6 ******\n This is a left-right style. You\u00e2\u0080\u0099ll note that there\u00e2\u0080\u0099s overlap of edges at\n the bottom \u00e2\u0080\u0093 a known issue with this display style.\n ***** With Contemporaneous Tips\u00c2\u00b6 *****\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-circular.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-circular.html", "unified_diff": "@@ -130,14 +130,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -24,9 +24,9 @@\n I modify values for the scale_bar placement and for label_pad. The latter\n controls the spacing between the tip ends and the label text.\n ***** Colouring a set of edges\u00c2\u00b6 *****\n \n ***** With Contemporaneous Tips\u00c2\u00b6 *****\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-radial.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-radial.html", "unified_diff": "@@ -125,14 +125,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -19,9 +19,9 @@\n                       # With_Contemporaneous_Tips\n [q                   ]\n \n ****** Radial Dendrogram Style\u00c2\u00b6 ******\n ***** With Contemporaneous Tips\u00c2\u00b6 *****\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-square.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-square.html", "unified_diff": "@@ -134,14 +134,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -28,9 +28,9 @@\n I change the scale bar placement. Valid values are \"top left\", \"top right\",\n \"bottom left\" (default), or \"bottom right\".\n ***** Colouring a set of edges\u00c2\u00b6 *****\n \n ***** With Contemporaneous Tips\u00c2\u00b6 *****\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-support.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-support.html", "unified_diff": "@@ -128,14 +128,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -28,9 +28,9 @@\n The support text is positioned relative to the x, y coordinates of the tree\n node. Control over support text placement is achieved using the support_xshift\n and support_yshift attributes. These are expressed in terms of pixels.\n To place the support text internal to the node, we set the yshift=0 (so at the\n same y-value of the node) and xshift it to the right using a positive integer.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/align_codons_to_protein.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/align_codons_to_protein.html", "unified_diff": "@@ -134,14 +134,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -44,9 +44,9 @@\n we\u00e2\u0080\u0099ll get an error.\n The translated seqs can then be written to file, using the method write. That\n file then serves as input for an alignment program. The resulting alignment\n file can be read back in. (We won\u00e2\u0080\u0099t write to file in this example.) For this\n example we will specify the aligned sequences in the dict, rather than from\n file.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/calculate_UPGMA_cluster.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/calculate_UPGMA_cluster.html", "unified_diff": "@@ -140,14 +140,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -30,9 +30,9 @@\n Import a substitution model (or create your own)\n Load the alignment.\n Create a pairwise distances object calculator for the alignment, providing a\n substitution model instance.\n Now use this matrix to build a UPGMA cluster.\n We demonstrate saving this UPGMA cluster to a file.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/calculate_neigbourjoining_tree.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/calculate_neigbourjoining_tree.html", "unified_diff": "@@ -136,14 +136,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -28,9 +28,9 @@\n Import a substitution model (or create your own)\n Load the alignment.\n Create a pairwise distances object calculator for the alignment, providing a\n substitution model instance.\n Now use this matrix to build a neighbour joining tree.\n We can save this tree to file.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/calculate_pairwise_distances.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/calculate_pairwise_distances.html", "unified_diff": "@@ -137,14 +137,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -31,9 +31,9 @@\n and run it.\n Note that pairwise distances can be distributed for computation across multiple\n CPU\u00e2\u0080\u0099s. In this case, when statistics (like distances) are requested only the\n master CPU returns data.\n We\u00e2\u0080\u0099ll write a phylip formatted distance matrix.\n We\u00e2\u0080\u0099ll also save the distances to file in Python\u00e2\u0080\u0099s pickle format.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/codon_models.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/codon_models.html", "unified_diff": "@@ -232,14 +232,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -178,9 +178,9 @@\n  HowlerMon    2a     0.00\n  HowlerMon    2b     1.00\n     Rhesus     0     0.00\n     Rhesus     1     1.00\n     ...\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/coevolution.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/coevolution.html", "unified_diff": "@@ -139,14 +139,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -58,9 +58,9 @@\n Briefly, sequence identifiers are split on + symbols. The ids before the + must\n match perfectly between the two alignments as these are used to match the\n sequences between alignments. In the following example, these are common\n species names: human, chicken, echidna, and pig. The text after the + can be\n anything, and should probably be the original database identifiers of the\n sequences.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/complete_seq_features.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/complete_seq_features.html", "unified_diff": "@@ -166,14 +166,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -86,9 +86,9 @@\n We add annotations to the sequences as a series.\n We add the annotations to the sequences one segment at a time.\n These different constructions should generate the same output.\n Annotations should be correctly masked, whether the sequence has been reverse\n complemented or not. We use the plus/minus strand CDS containing sequences\n created above.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/empirical_protein_models.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/empirical_protein_models.html", "unified_diff": "@@ -137,14 +137,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -36,9 +36,9 @@\n letter amino acid name order white space delineated followed by motif\n frequencies in the same order.\n Create an Empirical Protein Matrix Substitution model object. This will take\n the unscaled empirical matrix and use it and the motif frequencies to create a\n scaled Q matrix.\n Make a parameter controller, likelihood function object and optimise.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/hmm_par_heterogeneity.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/hmm_par_heterogeneity.html", "unified_diff": "@@ -166,14 +166,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -99,9 +99,9 @@\n At the same time we set the upper/lower bin boundaries.\n We then illustrate how to adjust the bin probabilities, here doing it so that\n one of them is nearly 1, the other nearly 0. This ensures the likelihood will\n be near identical to that of lf_one and as a result the optimisation step will\n actually improve fit over the simpler model.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/index.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/index.html", "unified_diff": "@@ -198,14 +198,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -60,9 +60,9 @@\n     * Make_a_UPGMA_cluster\n     * Phylogenetic_reconstruction_by_least_squares\n \n ***** Utilities\u00c2\u00b6 *****\n     * Parallel_computations\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/manipulating_tree_nodes.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/manipulating_tree_nodes.html", "unified_diff": "@@ -160,14 +160,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -84,9 +84,9 @@\n append to the deletion list if greater than 1.8.\n Now for the actual deletion process. We can simply use the parent of each node\n in the deletion list to remove itself. Pruning is necessary to prevent internal\n nodes from being left as tips. Note: remove() and remove_node() return\n \u00e2\u0080\u0098True\u00e2\u0080\u0099 if a node is successfully removed, \u00e2\u0080\u0098False\u00e2\u0080\u0099 otherwise.\n Finally, print the modified complex_tree.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/neutral_test.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/neutral_test.html", "unified_diff": "@@ -144,14 +144,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -50,9 +50,9 @@\n likelihood parameter estimates attached to each tree edge. This object can be\n used for plotting, or to provide starting estimates to a related model.\n The lnL\u00e2\u0080\u0099s from the two models are now used to calculate the likelihood ratio\n statistic (LR) it\u00e2\u0080\u0099s degrees-of-freedom (df) and the probability (P) of\n observing the LR.\n Print this and look up a chi-sq with number of edges - 1 degrees of freedom.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/parallel.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/parallel.html", "unified_diff": "@@ -325,14 +325,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -236,9 +236,9 @@\n This environment variable is created by the PBS system on executing the job\n script.\n   [3]\n You can check your execution of the script is correct by validating you get all\n the ranks up to one minus the number of CPUs you requested.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/parametric_bootstrap.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/parametric_bootstrap.html", "unified_diff": "@@ -141,14 +141,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -42,9 +42,9 @@\n Specify how many random samples we want it to generate. Here we use a very\n small number of replicates only for the purpose of testing.\n Run it.\n Get the estimated probability.\n p is a floating point value, as you\u00e2\u0080\u0099d expect. Grab the estimated likelihoods\n (null and alternate) for the observed data.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/period_estimation.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/period_estimation.html", "unified_diff": "@@ -218,14 +218,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -107,9 +107,9 @@\n Note\n We defined the period length of interest in defining this calculator because\n we\u00e2\u0080\u0099re interested in dinucleotide motifs.\n We then construct a seq-to-symbol convertor.\n The rest is as per the analysis using Goertzel above.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/phylo_by_ls.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/phylo_by_ls.html", "unified_diff": "@@ -169,14 +169,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -92,9 +92,9 @@\n substitution model (like a HKY85 for DNA or JTT92 for protein), and an\n alignment. It also optionally takes a distance matrix, such as that used here,\n computed for the same sequences. These distances are then used to obtain\n estimates of branch lengths by the WLS method for each evaluated tree topology\n which are then used as starting values for the likelihood optimisation.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/rate_heterogeneity.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/rate_heterogeneity.html", "unified_diff": "@@ -135,14 +135,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -31,9 +31,9 @@\n concatenate them to create a new alignment.\n Start from scratch, optimising only rates and the rate probability ratio.\n We want to know the bin probabilities and the posterior probabilities.\n We\u00e2\u0080\u0099ll now use a gamma distribution on the sample alignment, specifying the\n number of bins as 4. We specify that the bins have equal density using the\n lf.set_param_rule('bprobs', is_constant=True) command.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/relative_rate.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/relative_rate.html", "unified_diff": "@@ -146,14 +146,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -43,9 +43,9 @@\n vector.\n View the resulting maximum-likelihood parameter values.\n These two lnL\u00e2\u0080\u0099s are now used to calculate the likelihood ratio statistic\n it\u00e2\u0080\u0099s degrees-of-freedom and the probability of observing the LR.\n Print this and look up a \\(\\chi^2\\) with number of edges - 1 degrees of\n freedom.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/scope_model_params_on_trees.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/scope_model_params_on_trees.html", "unified_diff": "@@ -220,14 +220,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -122,9 +122,9 @@\n is used for providing initial (starting) values for fitting.\n I\u00e2\u0080\u0099ll now free up omega on the primate clade, but making it a single value\n shared by all primate lineages.\n Finally I\u00e2\u0080\u0099ll allow all primate edges to have different values of omega.\n We now allow omega to be different on all edges.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/seq_features.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/seq_features.html", "unified_diff": "@@ -141,14 +141,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -48,9 +48,9 @@\n We can use this list to construct a pseudo-feature covering (or excluding)\n multiple features using get_region_covering_all. For instance, getting all\n exons,\n or not exons (the exon shadow):\n The first of these essentially returns the CDS of the gene.\n Features are themselves sliceable:\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/simple.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/simple.html", "unified_diff": "@@ -131,14 +131,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -24,9 +24,9 @@\n \n ****** The simplest script\u00c2\u00b6 ******\n Section author: Gavin Huttley\n We use a canned nucleotide substitution model (the HKY85 model) on just three\n primate species. As there is only one unrooted tree possible, the sequence\n names are all that\u00e2\u0080\u0099s required to make the tree.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/simulate_alignment.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/simulate_alignment.html", "unified_diff": "@@ -134,14 +134,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -26,9 +26,9 @@\n Section author: Gavin Huttley\n For this example we just create a simple model using a four taxon tree with\n different branch lengths and a Felsenstein model.\n Specify the 4 taxon tree,\n Define our Felsenstein 1981 substitution model.\n We\u00e2\u0080\u0099ll now create a simulated alignment of length 1000 nucleotides.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/testing_multi_loci.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/testing_multi_loci.html", "unified_diff": "@@ -134,14 +134,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -34,9 +34,9 @@\n To make a likelihood function with multiple alignments we provide the list of\n loci names. We can then specify a parameter (other than length) to be the same\n across the loci (using the imported ALL) or different for each locus (using\n EACH). We conduct a LR test as before.\n Just to pretty up the result display, I\u00e2\u0080\u0099ll print(a table consisting of the\n test statistics created on the fly.)\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/general.html", "source2": "./usr/share/doc/python-cogent-doc/html/general.html", "unified_diff": "@@ -130,14 +130,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -30,9 +30,9 @@\n ****** Support\u00c2\u00b6 ******\n We acknowledge the provision by Wingware of free licenses for their\n professional IDE. Their commitment, over more than a decade, to supporting our\n development of Open Source software for science is greatly appreciated. (The\n port of PyCogent to Python 3 was made much easier by using Wing\u00e2\u0080\u0099s refactor\n tools!)\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/genindex.html", "source2": "./usr/share/doc/python-cogent-doc/html/genindex.html", "unified_diff": "@@ -2219,14 +2219,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -562,9 +562,9 @@\n           o (ProteinSequence_method)        * write()_(Alignment_method)\n           o (RnaSequence_method)                  o (ArrayAlignment_method)\n     * with_modified_termini()_                    o (PhyloNode_method)\n       (Alignment_method)                          o (SequenceCollection_method)\n           o (ArrayAlignment_method)               o (Table_method)\n           o (SequenceCollection_method)\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/index.html", "source2": "./usr/share/doc/python-cogent-doc/html/index.html", "unified_diff": "@@ -128,14 +128,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -25,9 +25,9 @@\n framework for manipulation of genomic sequence data and for conducting\n molecular evolutionary analyses. It is distinguished by many unique built-in\n capabilities. Of particular note are our non-stationary Markov substitution\n models. These include non-stationary_nucleotide, and non-stationary_codon\n models.\n Plus, the ability to manipulate biological sequences by their annotations.\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/install.html", "source2": "./usr/share/doc/python-cogent-doc/html/install.html", "unified_diff": "@@ -184,14 +184,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -56,9 +56,9 @@\n Once the environment is active\n (c3-env) $ conda install jupyterlab # or pip install jupyterlab if you prefer\n then follow the instructions posted on the Plotly pipy page to install and\n configure Plotly for jupyter.\n Then install cogent3 using the variant of pip install from above that you want.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/licenses.html", "source2": "./usr/share/doc/python-cogent-doc/html/licenses.html", "unified_diff": "@@ -150,14 +150,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -43,9 +43,9 @@\n DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\n SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\n CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\n OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/pycogent.html", "source2": "./usr/share/doc/python-cogent-doc/html/pycogent.html", "unified_diff": "@@ -144,14 +144,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -53,9 +53,9 @@\n   cogent.seqsim\u00c2\u00b6\n       See the sequence simulation capabilities in cogent3.evolve and\n       cogent3.app.evo.\n   cogent.maths.unifrac\u00c2\u00b6\n       The microbiome related functions are now in scikit-bio.\n \n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/search.html", "source2": "./usr/share/doc/python-cogent-doc/html/search.html", "unified_diff": "@@ -140,14 +140,14 @@\n <footer class=\"footer\">\n   <div class=\"container\">\n     <p class=\"pull-right\">\n       <a href=\"#\">Back to top</a>\n       \n     </p>\n     <p>\n-        &copy; Copyright 2020-2025, cogent3 Team.<br/>\n+        &copy; Copyright 2020-2023, cogent3 Team.<br/>\n       Created using <a href=\"http://sphinx-doc.org/\">Sphinx</a> 7.2.6.<br/>\n     </p>\n   </div>\n </footer>\n   </body>\n </html>\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -20,9 +20,9 @@\n From here you can search these documents. Enter your search words into the box\n below and click \"search\". Note that the search function will automatically\n search for all of the words. Pages containing fewer words won't appear in the\n result list.\n [q                   ]\n [search]\n Back_to_top\n-\u00a9 Copyright 2020-2025, cogent3 Team.\n+\u00a9 Copyright 2020-2023, cogent3 Team.\n Created using Sphinx 7.2.6.\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/searchindex.js", "source2": "./usr/share/doc/python-cogent-doc/html/searchindex.js", "unified_diff": null, "details": [{"source1": "js-beautify {}", "source2": "js-beautify {}", "unified_diff": "@@ -1629,15 +1629,15 @@\n         \"compare_by_nam\": 38,\n         \"compare_by_subset\": 38,\n         \"exclude_absent_taxa\": 38,\n         \"compare_by_tip_dist\": 38,\n         \"dist_f\": 38,\n         \"distance_from_r\": 38,\n         \"shuffle_f\": 38,\n-        \"0x1421ab0\": 38,\n+        \"0xffbcb0\": 38,\n         \"m1\": 38,\n         \"m2\": 38,\n         \"pearson\": [38, 80],\n         \"correl\": [38, 80, 102],\n         \"coeffici\": 38,\n         \"madimum\": 38,\n         \"applic\": [38, 49, 66, 124],\n"}]}]}]}]}, {"source1": "python3-cogent3_2023.2.12a1+dfsg-4_amd64.deb", "source2": "python3-cogent3_2023.2.12a1+dfsg-4_amd64.deb", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -1,3 +1,3 @@\n--rw-r--r--   0        0        0        4 2025-01-26 17:32:12.000000 debian-binary\n--rw-r--r--   0        0        0    10436 2025-01-26 17:32:12.000000 control.tar.xz\n--rw-r--r--   0        0        0  1881628 2025-01-26 17:32:12.000000 data.tar.xz\n+-rw-r--r--   0        0        0        4 2023-12-25 11:51:52.000000 debian-binary\n+-rw-r--r--   0        0        0    10432 2023-12-25 11:51:52.000000 control.tar.xz\n+-rw-r--r--   0        0        0  1880920 2023-12-25 11:51:52.000000 data.tar.xz\n"}, {"source1": "control.tar.xz", "source2": "control.tar.xz", "unified_diff": null, "details": [{"source1": "control.tar", "source2": "control.tar", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -1,5 +1,5 @@\n-drwxr-xr-x   0 root         (0) root         (0)        0 2025-01-26 17:32:12.000000 ./\n--rw-r--r--   0 root         (0) root         (0)     1214 2025-01-26 17:32:12.000000 ./control\n--rw-r--r--   0 root         (0) root         (0)    36655 2025-01-26 17:32:12.000000 ./md5sums\n--rwxr-xr-x   0 root         (0) root         (0)      277 2025-01-26 17:32:12.000000 ./postinst\n--rwxr-xr-x   0 root         (0) root         (0)      390 2025-01-26 17:32:12.000000 ./prerm\n+drwxr-xr-x   0 root         (0) root         (0)        0 2023-12-25 11:51:52.000000 ./\n+-rw-r--r--   0 root         (0) root         (0)     1214 2023-12-25 11:51:52.000000 ./control\n+-rw-r--r--   0 root         (0) root         (0)    36655 2023-12-25 11:51:52.000000 ./md5sums\n+-rwxr-xr-x   0 root         (0) root         (0)      277 2023-12-25 11:51:52.000000 ./postinst\n+-rwxr-xr-x   0 root         (0) root         (0)      390 2023-12-25 11:51:52.000000 ./prerm\n"}, {"source1": "./md5sums", "source2": "./md5sums", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "comments": ["Files differ"], "unified_diff": null}]}]}]}, {"source1": "data.tar.xz", "source2": "data.tar.xz", "unified_diff": null, "details": [{"source1": "data.tar", "source2": "data.tar", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -1,260 +1,260 @@\n-drwxr-xr-x   0 root         (0) root         (0)        0 2025-01-26 17:32:12.000000 ./\n-drwxr-xr-x   0 root         (0) root         (0)        0 2025-01-26 17:32:12.000000 ./usr/\n-drwxr-xr-x   0 root         (0) root         (0)        0 2025-01-26 17:32:12.000000 ./usr/lib/\n-drwxr-xr-x   0 root         (0) root         (0)        0 2025-01-26 17:32:12.000000 ./usr/lib/python3/\n-drwxr-xr-x   0 root         (0) root         (0)        0 2025-01-26 17:32:12.000000 ./usr/lib/python3/dist-packages/\n-drwxr-xr-x   0 root         (0) 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