AUTHORS.rst
CHANGES.rst
LICENSE.rst
MANIFEST.in
README.rst
setup.py
applications/dendropy-format/dendropy-format
applications/sumlabels/sumlabels.py
applications/sumtrees/sumtrees.py
src/DendroPy.egg-info/PKG-INFO
src/DendroPy.egg-info/SOURCES.txt
src/DendroPy.egg-info/dependency_links.txt
src/DendroPy.egg-info/entry_points.txt
src/DendroPy.egg-info/requires.txt
src/DendroPy.egg-info/top_level.txt
src/DendroPy.egg-info/zip-safe
src/dendropy/__init__.py
src/dendropy/__main__.py
src/dendropy/calculate/__init__.py
src/dendropy/calculate/combinatorics.py
src/dendropy/calculate/mathfn.py
src/dendropy/calculate/phylogeneticdistance.py
src/dendropy/calculate/popgenstat.py
src/dendropy/calculate/probability.py
src/dendropy/calculate/profiledistance.py
src/dendropy/calculate/statistics.py
src/dendropy/calculate/treecompare.py
src/dendropy/calculate/treemeasure.py
src/dendropy/calculate/treescore.py
src/dendropy/calculate/treesum.py
src/dendropy/dataio/__init__.py
src/dendropy/dataio/fastareader.py
src/dendropy/dataio/fastawriter.py
src/dendropy/dataio/ioservice.py
src/dendropy/dataio/multiphylipreader.py
src/dendropy/dataio/newick.py
src/dendropy/dataio/newickreader.py
src/dendropy/dataio/newickwriter.py
src/dendropy/dataio/newickyielder.py
src/dendropy/dataio/nexmlreader.py
src/dendropy/dataio/nexmlwriter.py
src/dendropy/dataio/nexmlyielder.py
src/dendropy/dataio/nexusprocessing.py
src/dendropy/dataio/nexusreader.py
src/dendropy/dataio/nexuswriter.py
src/dendropy/dataio/nexusyielder.py
src/dendropy/dataio/phylipreader.py
src/dendropy/dataio/phylipwriter.py
src/dendropy/dataio/tokenizer.py
src/dendropy/dataio/xmlprocessing.py
src/dendropy/datamodel/__init__.py
src/dendropy/datamodel/basemodel.py
src/dendropy/datamodel/charmatrixmodel.py
src/dendropy/datamodel/charstatemodel.py
src/dendropy/datamodel/datasetmodel.py
src/dendropy/datamodel/taxonmodel.py
src/dendropy/datamodel/treecollectionmodel.py
src/dendropy/datamodel/treemodel/__init__.py
src/dendropy/datamodel/treemodel/_bipartition.py
src/dendropy/datamodel/treemodel/_edge.py
src/dendropy/datamodel/treemodel/_node.py
src/dendropy/datamodel/treemodel/_tree.py
src/dendropy/interop/__init__.py
src/dendropy/interop/ape.py
src/dendropy/interop/biopython.py
src/dendropy/interop/entrez.py
src/dendropy/interop/ete.py
src/dendropy/interop/gbif.py
src/dendropy/interop/genbank.py
src/dendropy/interop/itol.py
src/dendropy/interop/muscle.py
src/dendropy/interop/paup.py
src/dendropy/interop/raxml.py
src/dendropy/interop/rspr.py
src/dendropy/interop/rstats.py
src/dendropy/interop/seqgen.py
src/dendropy/legacy/__init__.py
src/dendropy/legacy/coalescent.py
src/dendropy/legacy/continuous.py
src/dendropy/legacy/ncbi.py
src/dendropy/legacy/popgensim.py
src/dendropy/legacy/popgenstat.py
src/dendropy/legacy/reconcile.py
src/dendropy/legacy/seqmodel.py
src/dendropy/legacy/seqsim.py
src/dendropy/legacy/treecalc.py
src/dendropy/legacy/treemanip.py
src/dendropy/legacy/treesim.py
src/dendropy/legacy/treesplit.py
src/dendropy/legacy/treesum.py
src/dendropy/mathlib/__init__.py
src/dendropy/mathlib/mathfn.py
src/dendropy/mathlib/probability.py
src/dendropy/mathlib/statistics.py
src/dendropy/model/__init__.py
src/dendropy/model/birthdeath.py
src/dendropy/model/coalescent.py
src/dendropy/model/continuous.py
src/dendropy/model/discrete.py
src/dendropy/model/multispeciescoalescent.py
src/dendropy/model/parsimony.py
src/dendropy/model/protractedspeciation.py
src/dendropy/model/reconcile.py
src/dendropy/model/treeshape.py
src/dendropy/simulate/__init__.py
src/dendropy/simulate/charsim.py
src/dendropy/simulate/popgensim.py
src/dendropy/simulate/treesim.py
src/dendropy/utility/__init__.py
src/dendropy/utility/bibtex.py
src/dendropy/utility/bitprocessing.py
src/dendropy/utility/cli.py
src/dendropy/utility/constants.py
src/dendropy/utility/container.py
src/dendropy/utility/debug.py
src/dendropy/utility/deprecate.py
src/dendropy/utility/error.py
src/dendropy/utility/filesys.py
src/dendropy/utility/messaging.py
src/dendropy/utility/metavar.py
src/dendropy/utility/processio.py
src/dendropy/utility/terminal.py
src/dendropy/utility/textprocessing.py
src/dendropy/utility/timeprocessing.py
src/dendropy/utility/urlio.py
src/dendropy/utility/vcsinfo.py
src/dendropy/utility/libexec/__init__.py
tests/data/chars/COII_Apes.nex
tests/data/chars/GEBA.chars.nexus
tests/data/chars/actinopterygii.chars.nexus
tests/data/chars/angiosperms.chars.nexus
tests/data/chars/angiosperms.chars.txt
tests/data/chars/apternodus.chars.hacked-for-tests.txt
tests/data/chars/apternodus.chars.interleaved.nexus
tests/data/chars/apternodus.chars.nexml
tests/data/chars/apternodus.chars.nexus
tests/data/chars/avian-ovomucoids.chars.nexus
tests/data/chars/avian-ovomucoids.chars.txt
tests/data/chars/bad_names.fasta
tests/data/chars/caenophidia_mos.chars.fasta
tests/data/chars/caenophidia_mos.chars.nexus
tests/data/chars/caenophidia_mos.chars.txt
tests/data/chars/cetaceans.nex
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tests/data/chars/pythonidae.chars.phylip
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tests/data/chars/pythonidae_continuous.chars.txt
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tests/data/chars/sfs_test_single_pop_100x500_01.sfs.unfolded.txt
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tests/data/chars/sfs_test_single_pop_100x500_09.sfs.folded.txt
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tests/data/chars/standard-test-chars-continuous.as_seqs.nexml
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tests/data/other/hiv1.distances.csv
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tests/data/other/laurasiatherian.distances.ml.csv
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tests/data/other/saitou_and_nei_1987_table1.csv
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