[med-svn] [python-dendropy] branch upstream updated (5ac580a -> 9278860)
Andreas Tille
tille at debian.org
Wed Jul 29 11:20:44 UTC 2015
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tille pushed a change to branch upstream
in repository python-dendropy.
from 5ac580a Imported Upstream version 4.0.2
new 9278860 Imported Upstream version 4.0.3
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
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Summary of changes:
CHANGES.rst | 15 +-
DendroPy.egg-info/PKG-INFO | 23 +-
DendroPy.egg-info/SOURCES.txt | 463 +
LICENSE.rst | 104 +-
MANIFEST.in | 1 +
PKG-INFO | 23 +-
README.rst | 19 +
applications/sumtrees/sumtrees.py | 25 +-
dendropy/__init__.py | 8 +-
dendropy/__main__.py | 4 +-
dendropy/calculate/__init__.py | 4 +-
dendropy/calculate/mathfn.py | 4 +-
dendropy/calculate/popgenstat.py | 4 +-
dendropy/calculate/probability.py | 4 +-
dendropy/calculate/statistics.py | 4 +-
dendropy/calculate/treecompare.py | 4 +-
dendropy/calculate/treemeasure.py | 4 +-
dendropy/calculate/treescore.py | 5 +-
dendropy/calculate/treesum.py | 4 +-
dendropy/dataio/__init__.py | 4 +-
dendropy/dataio/fastareader.py | 4 +-
dendropy/dataio/fastawriter.py | 4 +-
dendropy/dataio/ioservice.py | 4 +-
dendropy/dataio/newick.py | 4 +-
dendropy/dataio/newickreader.py | 4 +-
dendropy/dataio/newickwriter.py | 4 +-
dendropy/dataio/newickyielder.py | 4 +-
dendropy/dataio/nexmlreader.py | 4 +-
dendropy/dataio/nexmlwriter.py | 4 +-
dendropy/dataio/nexmlyielder.py | 4 +-
dendropy/dataio/nexusprocessing.py | 5 +-
dendropy/dataio/nexusreader.py | 5 +-
dendropy/dataio/nexuswriter.py | 10 +-
dendropy/dataio/nexusyielder.py | 4 +-
dendropy/dataio/phylipreader.py | 4 +-
dendropy/dataio/phylipwriter.py | 4 +-
dendropy/dataio/tokenizer.py | 4 +-
dendropy/dataio/xmlprocessing.py | 4 +-
dendropy/datamodel/__init__.py | 4 +-
dendropy/datamodel/basemodel.py | 4 +-
dendropy/datamodel/charmatrixmodel.py | 8 +-
dendropy/datamodel/charstatemodel.py | 4 +-
dendropy/datamodel/datasetmodel.py | 4 +-
dendropy/datamodel/taxonmodel.py | 4 +-
dendropy/datamodel/treecollectionmodel.py | 17 +-
dendropy/datamodel/treemodel.py | 12 +-
dendropy/interop/__init__.py | 4 +-
dendropy/interop/ape.py | 4 +-
dendropy/interop/biopython.py | 4 +-
dendropy/interop/entrez.py | 4 +-
dendropy/interop/ete.py | 4 +-
dendropy/interop/gbif.py | 4 +-
dendropy/interop/genbank.py | 4 +-
dendropy/interop/muscle.py | 4 +-
dendropy/interop/paup.py | 6 +-
dendropy/interop/raxml.py | 4 +-
dendropy/interop/rstats.py | 22 +-
dendropy/interop/seqgen.py | 4 +-
dendropy/legacy/__init__.py | 4 +-
dendropy/legacy/coalescent.py | 4 +-
dendropy/legacy/continuous.py | 4 +-
dendropy/legacy/ncbi.py | 4 +-
dendropy/legacy/popgensim.py | 4 +-
dendropy/legacy/popgenstat.py | 4 +-
dendropy/legacy/reconcile.py | 4 +-
dendropy/legacy/seqmodel.py | 4 +-
dendropy/legacy/seqsim.py | 4 +-
dendropy/legacy/treecalc.py | 4 +-
dendropy/legacy/treemanip.py | 4 +-
dendropy/legacy/treesim.py | 4 +-
dendropy/legacy/treesplit.py | 4 +-
dendropy/legacy/treesum.py | 4 +-
dendropy/mathlib/__init__.py | 4 +-
dendropy/mathlib/mathfn.py | 4 +-
dendropy/mathlib/probability.py | 4 +-
dendropy/mathlib/statistics.py | 4 +-
dendropy/model/__init__.py | 19 +
dendropy/model/birthdeath.py | 288 +-
dendropy/model/coalescent.py | 49 +-
dendropy/model/continuous.py | 4 +-
dendropy/model/discrete.py | 4 +-
dendropy/model/parsimony.py | 120 +-
dendropy/model/protractedspeciation.py | 522 +
dendropy/model/reconcile.py | 4 +-
dendropy/model/treeshape.py | 4 +-
dendropy/simulate/__init__.py | 4 +-
dendropy/simulate/charsim.py | 4 +-
dendropy/simulate/popgensim.py | 4 +-
dendropy/simulate/treesim.py | 4 +-
dendropy/test/__init__.py | 4 +-
dendropy/test/__main__.py | 23 +-
dendropy/test/base_newick_test_cases.py | 4 +-
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dendropy/test/benchmark/__init__.py | 4 +-
.../benchmark_newick_light_tree_parser.py | 4 +-
.../test/benchmark/benchmark_newick_tree_parser.py | 5 +-
dendropy/test/benchmark/benchmark_tokenizer.py | 4 +-
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dendropy/test/data/chars/angiosperms.chars.nexus | 42 +
dendropy/test/data/chars/angiosperms.chars.txt | 34 +
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.../data/chars/apternodus.chars.interleaved.nexus | 69 +
dendropy/test/data/chars/apternodus.chars.nexml | 3821 +
dendropy/test/data/chars/apternodus.chars.nexus | 42 +
.../test/data/chars/avian-ovomucoids.chars.nexus | 203 +
.../test/data/chars/avian-ovomucoids.chars.txt | 89 +
dendropy/test/data/chars/bad_names.fasta | 10 +
.../test/data/chars/caenophidia_mos.chars.fasta | 228 +
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dendropy/test/data/chars/caenophidia_mos.chars.txt | 114 +
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dendropy/test/data/chars/orti.nex | 277 +
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...-None.use-tree-weights-None.burnin-0.splits.txt | 379 +
...-None.use-tree-weights-True.burnin-0.splits.txt | 379 +
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dendropy/test/data/trees/APG_Angiosperms.newick | 1 +
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dendropy/test/data/trees/cetaceans.taxa.nex | 29 +
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dendropy/test/data/trees/deepcoal1.nex | 77 +
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...est-trees-multifurcating-rooted-annotated.nexus | 105 +
...g-rooted-annotated.nexus-metadata-comments.json | 1740 +
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...endropy-test-trees-multifurcating-unrooted.json | 16358 +++
...dropy-test-trees-multifurcating-unrooted.newick | 10 +
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...ted-annotated-x10a.nexus-metadata-comments.json | 1389 +
.../dendropy-test-trees-n33-unrooted-x100a.json | 132405 ++++++++++++++++++
.../dendropy-test-trees-n33-unrooted-x100a.newick | 100 +
.../dendropy-test-trees-n33-unrooted-x100a.nexml | 13048 ++
.../dendropy-test-trees-n33-unrooted-x100a.nexus | 248 +
.../dendropy-test-trees-n33-unrooted-x10a.json | 13245 ++
.../dendropy-test-trees-n33-unrooted-x10a.newick | 10 +
.../dendropy-test-trees-n33-unrooted-x10a.nexml | 1348 +
.../dendropy-test-trees-n33-unrooted-x10a.nexus | 68 +
.../dendropy-test-trees-n33-unrooted-x10b.json | 13245 ++
.../dendropy-test-trees-n33-unrooted-x10b.newick | 10 +
.../dendropy-test-trees-n33-unrooted-x10b.nexml | 1348 +
.../dendropy-test-trees-n33-unrooted-x10b.nexus | 68 +
dendropy/test/data/trees/feb032009.splits.csv | 370 +
dendropy/test/data/trees/feb032009.trees.newick | 100 +
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.../trees/incomplete_leaves_rooted.pre-pruned.nex | 732 +
.../trees/incomplete_leaves_rooted.pruned_taxa.txt | 30 +
.../incomplete_leaves_rooted.retained_taxa.txt | 30 +
.../incomplete_leaves_unrooted.dendropy-pruned.nex | 732 +
.../incomplete_leaves_unrooted.paup-pruned.nex | 732 +
.../incomplete_leaves_unrooted.pre-pruned.nex | 732 +
.../incomplete_leaves_unrooted.pruned_taxa.txt | 30 +
.../incomplete_leaves_unrooted.retained_taxa.txt | 30 +
.../data/trees/issue_mth_2009-02-03.rooted.nexus | 229 +
.../data/trees/issue_mth_2009-02-03.unrooted.nexus | 229 +
dendropy/test/data/trees/maj-rule-bug1.trees.nexus | 229 +
dendropy/test/data/trees/maj-rule-bug2.trees.nexus | 233 +
dendropy/test/data/trees/multitreeblocks.nex | 28 +
dendropy/test/data/trees/multitreeblocks2.nex | 29 +
.../test/data/trees/primates.beast.mcct.meanh.tre | 37 +
.../data/trees/primates.beast.mcct.medianh.tre | 37 +
.../data/trees/primates.beast.mcct.noedgelens.tree | 25 +
dendropy/test/data/trees/primates.beast.mcmc.trees | 4037 +
dendropy/test/data/trees/primates.trees.nexus | 19 +
.../data/trees/prune_rooted.dendropy-pruned.nex | 732 +
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.../test/data/trees/pythonidae.annotated.nexml | 762 +
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.../test/data/trees/pythonidae.beast.summary.tre | 79 +
dendropy/test/data/trees/pythonidae.mb.con | 85 +
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.../test/data/trees/pythonidae.mlboots.newick.tre | 1001 +
.../test/data/trees/pythonidae.mlboots.nexus.tre | 1046 +
dendropy/test/data/trees/pythonidae.mle.newick | 1 +
.../test/data/trees}/pythonidae.mle.nex | 0
.../pythonidae.random.bd0301.midpoint-rooted.tre | 112 +
.../pythonidae.random.bd0301.randomly-rooted.tre | 145 +
.../test/data/trees}/pythonidae.random.bd0301.tre | 0
.../data/trees/pythonidae.reference-trees.newick | 11 +
.../data/trees/pythonidae.reference-trees.nexus | 89 +
.../pythonidae.reference-trees.no-taxa-block.nexus | 50 +
...eference-trees.no-taxa-no-translate-block.nexus | 17 +
...nidae.reference-trees.taxon-numbers-only.newick | 11 +
dendropy/test/data/trees/rana.trees.nexus | 70 +
dendropy/test/data/trees/treebase_s373.xml | 634 +
dendropy/test/support/__init__.py | 19 +
dendropy/test/support/compare_and_validate.py | 4 +-
dendropy/test/support/coverage_analysis.py | 4 +-
dendropy/test/support/curated_dataset.py | 4 +-
dendropy/test/support/curated_test_tree.py | 4 +-
dendropy/test/support/curated_test_tree_list.py | 4 +-
dendropy/test/support/dendropytest.py | 4 +-
dendropy/test/support/mockrandom.py | 4 +-
dendropy/test/support/mockreader.py | 18 +
dendropy/test/support/pathmap.py | 7 +-
dendropy/test/support/paupsplitsreference.py | 4 +-
dendropy/test/support/standard_file_test_chars.py | 16 +
.../test/support/standard_file_test_datasets.py | 4 +-
dendropy/test/support/standard_file_test_trees.py | 4 +-
dendropy/test/test_asciitree.py | 4 +-
dendropy/test/test_birthdeath.py | 4 +-
dendropy/test/test_coalescent.py | 4 +-
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dendropy/test/test_container_ordered_set.py | 4 +-
dendropy/test/test_continuous.py | 4 +-
dendropy/test/test_dataio_basic_tree.py | 17 +
dendropy/test/test_dataio_fasta_reader.py | 4 +-
dendropy/test/test_dataio_fasta_writer.py | 4 +-
dendropy/test/test_dataio_newick_reader_rooting.py | 4 +-
dendropy/test/test_dataio_newick_reader_tree.py | 4 +-
.../test/test_dataio_newick_reader_tree_iter.py | 4 +-
.../test/test_dataio_newick_reader_tree_list.py | 4 +-
dendropy/test/test_dataio_newick_writer.py | 4 +-
dendropy/test/test_dataio_nexml_reader_chars.py | 4 +-
.../test/test_dataio_nexml_reader_tree_list.py | 4 +-
dendropy/test/test_dataio_nexml_writer_chars.py | 4 +-
dendropy/test/test_dataio_nexml_writer_trees.py | 4 +-
dendropy/test/test_dataio_nexus_reader_chars.py | 4 +-
dendropy/test/test_dataio_nexus_reader_dataset.py | 4 +-
.../test/test_dataio_nexus_reader_tree_list.py | 4 +-
dendropy/test/test_dataio_nexus_taxon_handling.py | 4 +-
dendropy/test/test_dataio_nexus_tree_yielder.py | 4 +-
dendropy/test/test_dataio_nexus_writer_chars.py | 4 +-
dendropy/test/test_dataio_nexus_writer_dataset.py | 4 +-
dendropy/test/test_dataio_nexus_writer_tree.py | 4 +-
.../test/test_dataio_nexus_writer_tree_list.py | 4 +-
dendropy/test/test_dataio_phylip_reader_chars.py | 4 +-
dendropy/test/test_dataio_phylip_writer_chars.py | 4 +-
dendropy/test/test_dataio_tokenizer.py | 4 +-
dendropy/test/test_datamodel_annotations.py | 4 +-
dendropy/test/test_datamodel_bipartitions.py | 4 +-
dendropy/test/test_datamodel_charmatrix.py | 4 +-
dendropy/test/test_datamodel_dataset.py | 4 +-
dendropy/test/test_datamodel_split_bitmasks.py | 225 +-
dendropy/test/test_datamodel_statealphabet.py | 4 +-
dendropy/test/test_datamodel_taxon.py | 4 +-
...model_tree_construction_copying_and_identity.py | 4 +-
.../test/test_datamodel_tree_edge_fundamentals.py | 4 +-
dendropy/test/test_datamodel_tree_list.py | 4 +-
.../test/test_datamodel_tree_node_fundamentals.py | 4 +-
.../test_datamodel_tree_structure_and_iteration.py | 4 +-
.../test/test_datamodel_tree_taxon_management.py | 4 +-
dendropy/test/test_datamodel_treearray.py | 4 +-
dendropy/test/test_fitch.py | 7 +-
dendropy/test/test_parsimony_scoring.py | 494 +
dendropy/test/test_paup.py | 4 +-
dendropy/test/test_popgenstat.py | 26 +-
dendropy/test/test_statistics.py | 4 +-
.../test/test_tree_calculations_and_metrics.py | 4 +-
dendropy/test/test_tree_from_splits.py | 4 +-
.../test/test_tree_operations_and_manipulations.py | 5 +-
.../test_tree_reconciliation_and_discordance.py | 24 +-
dendropy/test/test_tree_split_compatibility.py | 4 +-
.../test/test_tree_summarization_and_consensus.py | 4 +-
dendropy/utility/__init__.py | 4 +-
dendropy/utility/bibtex.py | 4 +-
dendropy/utility/bitprocessing.py | 4 +-
dendropy/utility/cli.py | 4 +-
dendropy/utility/constants.py | 4 +-
dendropy/utility/container.py | 4 +-
dendropy/utility/debug.py | 4 +-
dendropy/utility/deprecate.py | 4 +-
dendropy/utility/error.py | 4 +-
dendropy/utility/filesys.py | 4 +-
dendropy/utility/libexec/__init__.py | 5 +-
dendropy/utility/messaging.py | 4 +-
dendropy/utility/metavar.py | 4 +-
dendropy/utility/processio.py | 4 +-
dendropy/utility/terminal.py | 18 +
dendropy/utility/textprocessing.py | 7 +-
dendropy/utility/timeprocessing.py | 4 +-
dendropy/utility/urlio.py | 4 +-
dendropy/utility/vcsinfo.py | 4 +-
doc/source/license.inc | 20 +-
doc/source/programs/sumtrees.rst | 2 +-
setup.py | 4 +-
650 files changed, 601289 insertions(+), 833 deletions(-)
create mode 100644 dendropy/model/protractedspeciation.py
create mode 100644 dendropy/test/data/chars/COII_Apes.nex
create mode 100644 dendropy/test/data/chars/GEBA.chars.nexus
create mode 100644 dendropy/test/data/chars/actinopterygii.chars.nexus
create mode 100644 dendropy/test/data/chars/angiosperms.chars.nexus
create mode 100644 dendropy/test/data/chars/angiosperms.chars.txt
create mode 100644 dendropy/test/data/chars/apternodus.chars.hacked-for-tests.txt
create mode 100644 dendropy/test/data/chars/apternodus.chars.interleaved.nexus
create mode 100644 dendropy/test/data/chars/apternodus.chars.nexml
create mode 100644 dendropy/test/data/chars/apternodus.chars.nexus
create mode 100644 dendropy/test/data/chars/avian-ovomucoids.chars.nexus
create mode 100644 dendropy/test/data/chars/avian-ovomucoids.chars.txt
create mode 100644 dendropy/test/data/chars/bad_names.fasta
create mode 100644 dendropy/test/data/chars/caenophidia_mos.chars.fasta
create mode 100644 dendropy/test/data/chars/caenophidia_mos.chars.nexus
create mode 100644 dendropy/test/data/chars/caenophidia_mos.chars.txt
create mode 100644 dendropy/test/data/chars/cetaceans.nex
create mode 100644 dendropy/test/data/chars/codons.nexml
create mode 100644 dendropy/test/data/chars/crotaphytus_bicinctores.cytb.aligned.nexml
create mode 100644 dendropy/test/data/chars/crotaphytus_bicinctores.nd2.aligned.nexml
create mode 100644 dendropy/test/data/chars/interleaved-charsets-all.nex
create mode 100644 dendropy/test/data/chars/interleaved-charsets-c1.nex
create mode 100644 dendropy/test/data/chars/interleaved-charsets-c2.nex
create mode 100644 dendropy/test/data/chars/interleaved-charsets-c3.nex
create mode 100644 dendropy/test/data/chars/orti.nex
create mode 100644 dendropy/test/data/chars/primates.chars.csv
create mode 100644 dendropy/test/data/chars/primates.chars.fasta
copy {doc/source/examples => dendropy/test/data/chars}/primates.chars.interleaved.nexus (100%)
copy {doc/source/examples => dendropy/test/data/chars}/primates.chars.nexus (100%)
copy {doc/source/examples => dendropy/test/data/chars}/primates.chars.simple.interleaved.nexus (100%)
copy {doc/source/examples => dendropy/test/data/chars}/primates.chars.simple.nexus (100%)
copy {doc/source/examples => dendropy/test/data/chars}/primates.chars.subsets-1stpos.nexus (100%)
copy {doc/source/examples => dendropy/test/data/chars}/primates.chars.subsets-2ndpos.nexus (100%)
copy {doc/source/examples => dendropy/test/data/chars}/primates.chars.subsets-3rdpos.nexus (100%)
copy {doc/source/examples => dendropy/test/data/chars}/primates.chars.subsets-all.nexus (100%)
copy {doc/source/examples => dendropy/test/data/chars}/primates.chars.subsets-coding.nexus (100%)
copy {doc/source/examples => dendropy/test/data/chars}/primates.chars.subsets-noncoding.nexus (100%)
create mode 100644 dendropy/test/data/chars/pythonidae.chars.beast.calibrated.xml
create mode 100644 dendropy/test/data/chars/pythonidae.chars.beast.uncalibrated.xml
copy doc/source/examples/pythonidae.fasta => dendropy/test/data/chars/pythonidae.chars.fasta (100%)
create mode 100644 dendropy/test/data/chars/pythonidae.chars.interleaved.nexus
copy {doc/source/examples => dendropy/test/data/chars}/pythonidae.chars.nexus (100%)
copy {doc/source/examples => dendropy/test/data/chars}/pythonidae.chars.phylip (100%)
create mode 100644 dendropy/test/data/chars/pythonidae.chars.txt
copy {doc/source/examples => dendropy/test/data/chars}/pythonidae_continuous.chars.nexml (100%)
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create mode 100644 dendropy/test/data/chars/standard-test-chars-continuous.interleaved.phylip
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create mode 100644 dendropy/test/data/chars/standard-test-chars-continuous.mesquite.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-continuous.relaxed.phylip
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create mode 100644 dendropy/test/data/chars/standard-test-chars-dna.interleaved.nexus
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create mode 100644 dendropy/test/data/chars/standard-test-chars-dna.multi.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-dna.relaxed.phylip
create mode 100644 dendropy/test/data/chars/standard-test-chars-dna.simple.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-generic.as_cells.nexml
create mode 100644 dendropy/test/data/chars/standard-test-chars-generic.as_seqs.nexml
create mode 100644 dendropy/test/data/chars/standard-test-chars-generic.basic.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-generic.dotted.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-generic.interleaved.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-generic.relaxed.phylip
create mode 100644 dendropy/test/data/chars/standard-test-chars-generic.simple.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-multiple-char-blocks.1.basic.nexus
copy dendropy/{model/__init__.py => test/data/chars/standard-test-chars-multiple.as_cells.nexml} (100%)
copy dendropy/{model/__init__.py => test/data/chars/standard-test-chars-multiple.as_seqs.nexml} (100%)
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create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.as_seqs.nexml
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.basic.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.fasta
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.interleaved.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.matchchar.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.multi.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.relaxed.phylip
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.simple.nexus
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create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.as_seqs.nexml
create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.basic.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.fasta
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create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.matchchar.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.multi.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.relaxed.phylip
create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.simple.nexus
create mode 100644 dendropy/test/data/mixed/GEBA.mixed.nexus
create mode 100644 dendropy/test/data/mixed/geospiza.nex
create mode 100644 dendropy/test/data/mixed/multitaxa_mesquite.nex
create mode 100644 dendropy/test/data/mixed/reference_single_taxonset_dataset.nex
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