CHANGES.rst
LICENSE.rst
MANIFEST.in
README.rst
setup.cfg
setup.py
DendroPy.egg-info/PKG-INFO
DendroPy.egg-info/SOURCES.txt
DendroPy.egg-info/dependency_links.txt
DendroPy.egg-info/entry_points.txt
DendroPy.egg-info/requires.txt
DendroPy.egg-info/top_level.txt
DendroPy.egg-info/zip-safe
applications/sumlabels/sumlabels.py
applications/sumtrees/sumtrees.py
dendropy/__init__.py
dendropy/__main__.py
dendropy/calculate/__init__.py
dendropy/calculate/combinatorics.py
dendropy/calculate/mathfn.py
dendropy/calculate/phylogeneticdistance.py
dendropy/calculate/popgenstat.py
dendropy/calculate/probability.py
dendropy/calculate/profiledistance.py
dendropy/calculate/statistics.py
dendropy/calculate/treecompare.py
dendropy/calculate/treemeasure.py
dendropy/calculate/treescore.py
dendropy/calculate/treesum.py
dendropy/dataio/__init__.py
dendropy/dataio/fastareader.py
dendropy/dataio/fastawriter.py
dendropy/dataio/ioservice.py
dendropy/dataio/newick.py
dendropy/dataio/newickreader.py
dendropy/dataio/newickwriter.py
dendropy/dataio/newickyielder.py
dendropy/dataio/nexmlreader.py
dendropy/dataio/nexmlwriter.py
dendropy/dataio/nexmlyielder.py
dendropy/dataio/nexusprocessing.py
dendropy/dataio/nexusreader.py
dendropy/dataio/nexuswriter.py
dendropy/dataio/nexusyielder.py
dendropy/dataio/phylipreader.py
dendropy/dataio/phylipwriter.py
dendropy/dataio/tokenizer.py
dendropy/dataio/xmlprocessing.py
dendropy/datamodel/__init__.py
dendropy/datamodel/basemodel.py
dendropy/datamodel/charmatrixmodel.py
dendropy/datamodel/charstatemodel.py
dendropy/datamodel/datasetmodel.py
dendropy/datamodel/taxonmodel.py
dendropy/datamodel/treecollectionmodel.py
dendropy/datamodel/treemodel.py
dendropy/interop/__init__.py
dendropy/interop/ape.py
dendropy/interop/biopython.py
dendropy/interop/entrez.py
dendropy/interop/ete.py
dendropy/interop/gbif.py
dendropy/interop/genbank.py
dendropy/interop/muscle.py
dendropy/interop/paup.py
dendropy/interop/raxml.py
dendropy/interop/rspr.py
dendropy/interop/rstats.py
dendropy/interop/seqgen.py
dendropy/legacy/__init__.py
dendropy/legacy/coalescent.py
dendropy/legacy/continuous.py
dendropy/legacy/ncbi.py
dendropy/legacy/popgensim.py
dendropy/legacy/popgenstat.py
dendropy/legacy/reconcile.py
dendropy/legacy/seqmodel.py
dendropy/legacy/seqsim.py
dendropy/legacy/treecalc.py
dendropy/legacy/treemanip.py
dendropy/legacy/treesim.py
dendropy/legacy/treesplit.py
dendropy/legacy/treesum.py
dendropy/mathlib/__init__.py
dendropy/mathlib/mathfn.py
dendropy/mathlib/probability.py
dendropy/mathlib/statistics.py
dendropy/model/__init__.py
dendropy/model/birthdeath.py
dendropy/model/coalescent.py
dendropy/model/continuous.py
dendropy/model/discrete.py
dendropy/model/multispeciescoalescent.py
dendropy/model/parsimony.py
dendropy/model/protractedspeciation.py
dendropy/model/reconcile.py
dendropy/model/treeshape.py
dendropy/simulate/__init__.py
dendropy/simulate/charsim.py
dendropy/simulate/popgensim.py
dendropy/simulate/treesim.py
dendropy/test/__init__.py
dendropy/test/__main__.py
dendropy/test/base_newick_test_cases.py
dendropy/test/base_standard_trees_parsing_test_cases.py
dendropy/test/test_asciitree.py
dendropy/test/test_birthdeath.py
dendropy/test/test_coalescent.py
dendropy/test/test_container_frozen_ordered_dict.py
dendropy/test/test_container_normalized_bitmask_dict.py
dendropy/test/test_container_ordered_set.py
dendropy/test/test_continuous.py
dendropy/test/test_dataio_basic_tree.py
dendropy/test/test_dataio_fasta_reader.py
dendropy/test/test_dataio_fasta_writer.py
dendropy/test/test_dataio_newick_reader_rooting.py
dendropy/test/test_dataio_newick_reader_tree.py
dendropy/test/test_dataio_newick_reader_tree_iter.py
dendropy/test/test_dataio_newick_reader_tree_list.py
dendropy/test/test_dataio_newick_writer.py
dendropy/test/test_dataio_nexml_reader_chars.py
dendropy/test/test_dataio_nexml_reader_tree_list.py
dendropy/test/test_dataio_nexml_writer_chars.py
dendropy/test/test_dataio_nexml_writer_trees.py
dendropy/test/test_dataio_nexus_reader_chars.py
dendropy/test/test_dataio_nexus_reader_dataset.py
dendropy/test/test_dataio_nexus_reader_tree_list.py
dendropy/test/test_dataio_nexus_taxon_handling.py
dendropy/test/test_dataio_nexus_tree_yielder.py
dendropy/test/test_dataio_nexus_writer_chars.py
dendropy/test/test_dataio_nexus_writer_dataset.py
dendropy/test/test_dataio_nexus_writer_tree.py
dendropy/test/test_dataio_nexus_writer_tree_list.py
dendropy/test/test_dataio_phylip_reader_chars.py
dendropy/test/test_dataio_phylip_writer_chars.py
dendropy/test/test_dataio_tokenizer.py
dendropy/test/test_datamodel_annotations.py
dendropy/test/test_datamodel_bipartitions.py
dendropy/test/test_datamodel_charmatrix.py
dendropy/test/test_datamodel_dataset.py
dendropy/test/test_datamodel_split_bitmasks.py
dendropy/test/test_datamodel_statealphabet.py
dendropy/test/test_datamodel_taxon.py
dendropy/test/test_datamodel_tree_construction_copying_and_identity.py
dendropy/test/test_datamodel_tree_edge_fundamentals.py
dendropy/test/test_datamodel_tree_list.py
dendropy/test/test_datamodel_tree_node_fundamentals.py
dendropy/test/test_datamodel_tree_structure_and_iteration.py
dendropy/test/test_datamodel_tree_taxon_management.py
dendropy/test/test_datamodel_treearray.py
dendropy/test/test_fitch.py
dendropy/test/test_multispeciescoalescent.py
dendropy/test/test_parsimony_scoring.py
dendropy/test/test_paup.py
dendropy/test/test_phylogenetic_distance_matrix.py
dendropy/test/test_popgenstat.py
dendropy/test/test_protractedspeciation.py
dendropy/test/test_statistics.py
dendropy/test/test_tree_calculations_and_metrics.py
dendropy/test/test_tree_from_splits.py
dendropy/test/test_tree_operations_and_manipulations.py
dendropy/test/test_tree_reconciliation_and_discordance.py
dendropy/test/test_tree_shape_kernel.py
dendropy/test/test_tree_split_compatibility.py
dendropy/test/test_tree_summarization_and_consensus.py
dendropy/test/benchmark/__init__.py
dendropy/test/benchmark/benchmark_newick_light_tree_parser.py
dendropy/test/benchmark/benchmark_newick_tree_parser.py
dendropy/test/benchmark/benchmark_tokenizer.py
dendropy/test/data/chars/COII_Apes.nex
dendropy/test/data/chars/GEBA.chars.nexus
dendropy/test/data/chars/actinopterygii.chars.nexus
dendropy/test/data/chars/angiosperms.chars.nexus
dendropy/test/data/chars/angiosperms.chars.txt
dendropy/test/data/chars/apternodus.chars.hacked-for-tests.txt
dendropy/test/data/chars/apternodus.chars.interleaved.nexus
dendropy/test/data/chars/apternodus.chars.nexml
dendropy/test/data/chars/apternodus.chars.nexus
dendropy/test/data/chars/avian-ovomucoids.chars.nexus
dendropy/test/data/chars/avian-ovomucoids.chars.txt
dendropy/test/data/chars/bad_names.fasta
dendropy/test/data/chars/caenophidia_mos.chars.fasta
dendropy/test/data/chars/caenophidia_mos.chars.nexus
dendropy/test/data/chars/caenophidia_mos.chars.txt
dendropy/test/data/chars/cetaceans.nex
dendropy/test/data/chars/codons.nexml
dendropy/test/data/chars/community.data.tsv
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dendropy/test/data/chars/pythonidae_continuous.chars.nexml
dendropy/test/data/chars/pythonidae_continuous.chars.nexus
dendropy/test/data/chars/pythonidae_continuous.chars.txt
dendropy/test/data/chars/standard-test-chars-continuous.as_cells.nexml
dendropy/test/data/chars/standard-test-chars-continuous.as_seqs.nexml
dendropy/test/data/chars/standard-test-chars-continuous.interleaved.phylip
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dendropy/test/data/chars/standard-test-chars-continuous.mesquite.nexus
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dendropy/test/data/chars/standard-test-chars-dna.as_cells.nexml
dendropy/test/data/chars/standard-test-chars-dna.as_seqs.nexml
dendropy/test/data/chars/standard-test-chars-dna.basic.nexus
dendropy/test/data/chars/standard-test-chars-dna.fasta
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dendropy/test/data/chars/standard-test-chars-dna.matchchar.nexus
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dendropy/test/data/chars/standard-test-chars-generic.as_seqs.nexml
dendropy/test/data/chars/standard-test-chars-generic.basic.nexus
dendropy/test/data/chars/standard-test-chars-generic.dotted.nexus
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dendropy/test/data/chars/standard-test-chars-generic.relaxed.phylip
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dendropy/test/data/chars/standard-test-chars-multiple.as_cells.nexml
dendropy/test/data/chars/standard-test-chars-multiple.as_seqs.nexml
dendropy/test/data/chars/standard-test-chars-protein.as_cells.nexml
dendropy/test/data/chars/standard-test-chars-protein.as_seqs.nexml
dendropy/test/data/chars/standard-test-chars-protein.basic.nexus
dendropy/test/data/chars/standard-test-chars-protein.fasta
dendropy/test/data/chars/standard-test-chars-protein.interleaved.nexus
dendropy/test/data/chars/standard-test-chars-protein.matchchar.nexus
dendropy/test/data/chars/standard-test-chars-protein.multi.nexus
dendropy/test/data/chars/standard-test-chars-protein.relaxed.phylip
dendropy/test/data/chars/standard-test-chars-protein.simple.nexus
dendropy/test/data/chars/standard-test-chars-rna.as_cells.nexml
dendropy/test/data/chars/standard-test-chars-rna.as_seqs.nexml
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dendropy/test/data/chars/standard-test-chars-rna.fasta
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dendropy/test/data/other/hiv1.distances.csv
dendropy/test/data/other/hiv1.node-to-node-dists.csv
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dendropy/test/data/other/laurasiatherian.distances.ml.csv
dendropy/test/data/other/multispecies_coalescent_test_data.json
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doc/source/examples/seqgen.py
doc/source/examples/setroot1.py
doc/source/examples/sim_and_count_deepcoal1.py
doc/source/examples/sim_and_count_deepcoal2.py
doc/source/examples/splitfreq.py
doc/source/examples/splits_on_trees.py
doc/source/examples/symdiff1.py
doc/source/examples/symdiff2.py
doc/source/examples/taxa_mgmt1.py
doc/source/examples/taxa_mgmt1a.py
doc/source/examples/taxa_mgmt1b.py
doc/source/examples/taxa_mgmt2.py
doc/source/examples/taxa_mgmt3.py
doc/source/examples/taxa_mgmt4.py
doc/source/examples/taxa_mgmt5.py
doc/source/examples/taxon_labels1.py
doc/source/examples/taxon_labels2.py
doc/source/examples/taxon_labels2b.py
doc/source/examples/taxon_labels3.py
doc/source/examples/taxon_labels4.py
doc/source/examples/to_outgroup_position.py
doc/source/examples/tree_clone_and_prune_vs_extract.py
doc/source/examples/tree_copy1.py
doc/source/examples/tree_copy2.py
doc/source/examples/tree_evolve_char1.py
doc/source/examples/tree_evolve_char2.py
doc/source/examples/tree_extract1.py
doc/source/examples/tree_extract2.py
doc/source/examples/tree_extract3.py
doc/source/examples/tree_extract4.py
doc/source/examples/tree_iter1.py
doc/source/examples/tree_iter2.py
doc/source/examples/tree_length_crit.py
doc/source/examples/tree_list_add1.py
doc/source/examples/tree_list_copy1.py
doc/source/examples/tree_list_copy2.py
doc/source/examples/tree_list_copy3.py
doc/source/examples/tree_list_ops1.py
doc/source/examples/tree_list_ops2.py
doc/source/examples/tree_rootings1.py
doc/source/examples/treemeasures1.py
doc/source/examples/weightedrf1.py
doc/source/library/basemodel.rst
doc/source/library/birthdeath.rst
doc/source/library/charmatrixmodel.rst
doc/source/library/charstatemodel.rst
doc/source/library/coalescent.rst
doc/source/library/continuous.rst
doc/source/library/datasetmodel.rst
doc/source/library/discrete.rst
doc/source/library/index.rst
doc/source/library/parsimony.rst
doc/source/library/phylogeneticdistance.rst
doc/source/library/popgensim.rst
doc/source/library/popgenstat.rst
doc/source/library/probability.rst
doc/source/library/reconcile.rst
doc/source/library/statistics.rst
doc/source/library/taxonmodel.rst
doc/source/library/treecollectionmodel.rst
doc/source/library/treecompare.rst
doc/source/library/treemeasure.rst
doc/source/library/treemodel.rst
doc/source/library/treescore.rst
doc/source/library/treeshape.rst
doc/source/library/treesim.rst
doc/source/primer/bipartitions.rst
doc/source/primer/chars.rst
doc/source/primer/converting.rst
doc/source/primer/dataobjects.rst
doc/source/primer/datasets.rst
doc/source/primer/genbank.rst
doc/source/primer/index.rst
doc/source/primer/paup.rst
doc/source/primer/phylogenetic_character_analyses.rst
doc/source/primer/phylogenetic_distances.rst
doc/source/primer/popgenstats.rst
doc/source/primer/raxml.rst
doc/source/primer/reading_and_writing.rst
doc/source/primer/seqgen.rst
doc/source/primer/taxa.rst
doc/source/primer/taxa_partitions.rst
doc/source/primer/treecollections.rst
doc/source/primer/treemanips.rst
doc/source/primer/trees.rst
doc/source/primer/treesims.rst
doc/source/primer/treestats.rst
doc/source/primer/working_with_metadata_annotations.rst
doc/source/programs/index.rst
doc/source/programs/sumtrees.rst
doc/source/schemas/fasta.rst
doc/source/schemas/index.rst
doc/source/schemas/newick.rst
doc/source/schemas/nexml.rst
doc/source/schemas/nexus.rst
doc/source/schemas/phylip.rst
doc/source/schemas/interfaces/fasta_as_string.py
doc/source/schemas/interfaces/fasta_dataset_get.py
doc/source/schemas/interfaces/fasta_dataset_read.py
doc/source/schemas/interfaces/fasta_dnacharactermatrix_get.py
doc/source/schemas/interfaces/fasta_infinitesitescharactermatrix_get.py
doc/source/schemas/interfaces/fasta_proteincharactermatrix_get.py
doc/source/schemas/interfaces/fasta_restrictionsitescharactermatrix_get.py
doc/source/schemas/interfaces/fasta_rnacharactermatrix_get.py
doc/source/schemas/interfaces/fasta_standardcharactermatrix_get.py
doc/source/schemas/interfaces/fasta_write.py
doc/source/schemas/interfaces/newick_as_string.py
doc/source/schemas/interfaces/newick_dataset_get.py
doc/source/schemas/interfaces/newick_dataset_read.py
doc/source/schemas/interfaces/newick_tree_get.py
doc/source/schemas/interfaces/newick_tree_get_from_path.py
doc/source/schemas/interfaces/newick_tree_get_from_stream.py
doc/source/schemas/interfaces/newick_treearray_read.py
doc/source/schemas/interfaces/newick_treelist_get.py
doc/source/schemas/interfaces/newick_treelist_read.py
doc/source/schemas/interfaces/newick_write.py
doc/source/schemas/interfaces/nexml_chars_as_string.py
doc/source/schemas/interfaces/nexml_chars_write.py
doc/source/schemas/interfaces/nexml_dataset_as_string.py
doc/source/schemas/interfaces/nexml_dataset_get.py
doc/source/schemas/interfaces/nexml_dataset_read.py
doc/source/schemas/interfaces/nexml_dataset_write.py
doc/source/schemas/interfaces/nexml_dnacharactermatrix_get.py
doc/source/schemas/interfaces/nexml_infinitesitescharactermatrix_get.py
doc/source/schemas/interfaces/nexml_proteincharactermatrix_get.py
doc/source/schemas/interfaces/nexml_restrictionsitescharactermatrix_get.py
doc/source/schemas/interfaces/nexml_rnacharactermatrix_get.py
doc/source/schemas/interfaces/nexml_standardcharactermatrix_get.py
doc/source/schemas/interfaces/nexml_tree_get.py
doc/source/schemas/interfaces/nexml_treearray_get.py
doc/source/schemas/interfaces/nexml_treearray_read.py
doc/source/schemas/interfaces/nexml_treelist_get.py
doc/source/schemas/interfaces/nexml_treelist_read.py
doc/source/schemas/interfaces/nexml_trees_as_string.py
doc/source/schemas/interfaces/nexml_trees_write.py
doc/source/schemas/interfaces/nexus_chars_as_string.py
doc/source/schemas/interfaces/nexus_chars_write.py
doc/source/schemas/interfaces/nexus_dataset_as_string.py
doc/source/schemas/interfaces/nexus_dataset_get.py
doc/source/schemas/interfaces/nexus_dataset_read.py
doc/source/schemas/interfaces/nexus_dataset_write.py
doc/source/schemas/interfaces/nexus_dnacharactermatrix_get.py
doc/source/schemas/interfaces/nexus_infinitesitescharactermatrix_get.py
doc/source/schemas/interfaces/nexus_proteincharactermatrix_get.py
doc/source/schemas/interfaces/nexus_restrictionsitescharactermatrix_get.py
doc/source/schemas/interfaces/nexus_rnacharactermatrix_get.py
doc/source/schemas/interfaces/nexus_standardcharactermatrix_get.py
doc/source/schemas/interfaces/nexus_tree_get.py
doc/source/schemas/interfaces/nexus_tree_get_from_path.py
doc/source/schemas/interfaces/nexus_tree_get_from_stream.py
doc/source/schemas/interfaces/nexus_treearray_read.py
doc/source/schemas/interfaces/nexus_treelist_get.py
doc/source/schemas/interfaces/nexus_treelist_read.py
doc/source/schemas/interfaces/nexus_trees_as_string.py
doc/source/schemas/interfaces/nexus_trees_write.py
doc/source/schemas/interfaces/phylip_as_string.py
doc/source/schemas/interfaces/phylip_dataset_get.py
doc/source/schemas/interfaces/phylip_dataset_read.py
doc/source/schemas/interfaces/phylip_dnacharactermatrix_get.py
doc/source/schemas/interfaces/phylip_infinitesitescharactermatrix_get.py
doc/source/schemas/interfaces/phylip_proteincharactermatrix_get.py
doc/source/schemas/interfaces/phylip_restrictionsitescharactermatrix_get.py
doc/source/schemas/interfaces/phylip_rnacharactermatrix_get.py
doc/source/schemas/interfaces/phylip_standardcharactermatrix_get.py
doc/source/schemas/interfaces/phylip_write.py