DendroPy
A Python library for phylogenetic scripting, simulation, data processing and manipulation.
파일 탐색기
- bug_report.md
- feature_request.md
- ci.yaml
- requirements.in
- requirements.sh
- requirements.txt
- requirements37.in
- requirements37.sh
- requirements37.txt
- publish.sh
- dendropy3.png
- dendropy_icon.png
- dendropy_logo.png
- google-groups-logo1.png
- logo_cipres.gif
- nsf.gif
- Octocat.png
- rtd.css
- theme.conf
- rtd.css
- cleardiv.html
- logo.html
- side_supplemental.html
- theme.conf
- backlogged-fail-whitelist.txt
- bdtree_multi1.py
- bdtree_multi2.py
- bibtex_annotations1.py
- bibtex_annotations2.py
- bibtex_annotations3.py
- build_tree_programmatically.py
- char_mat_concat.py
- char_mat_concat2.py
- chars_access1.py
- chars_access2.py
- chars_access3.py
- chars_access4.py
- contained_coalescent1.py
- contained_coalescent2.py
- ds1.py
- ds2.py
- ds4.py
- ds5.py
- dsrw1.py
- dynamic_annotations1.py
- euctree.py
- find_taxon_node1.py
- find_taxon_node2.py
- hiv1.nexus
- ladderize.py
- ltt.py
- majrule.py
- mcct.py
- mrca.py
- mrca2.py
- node_ages1.py
- orti1994.nex
- paup_estimate_model.py
- paup_estimate_tree_ml.py
- paup_estimate_tree_nj.py
- pbhg.py
- pdm.py
- pdm_mpd0.py
- pdm_mpd1.py
- pdm_nj_tree.py
- pdm_ses1.py
- pdm_ses2.py
- pdm_ses3.py
- pdm_tns1.py
- pdm_upgma_tree.py
- pgstats1.py
- pic1.py
- pic2.py
- pic3.py
- pic4.py
- pic_annotated.py
- preorder_filtered_edge_iteration.py
- preorder_filtered_node_iteration.py
- primates.cc.combined.nex
- primates.cc.nex
- primates.cc.tre
- primates.chars.interleaved.nexus
- primates.chars.nexus
- primates.chars.simple.interleaved.nexus
- primates.chars.simple.nexus
- primates.chars.subsets-1stpos.nexus
- primates.chars.subsets-2ndpos.nexus
- primates.chars.subsets-3rdpos.nexus
- primates.chars.subsets-all.nexus
- primates.chars.subsets-coding.nexus
- primates.chars.subsets-noncoding.nexus
- prune_taxa_with_labels.py
- pure_kingman1.py
- pythonidae.beast-mcmc.trees
- pythonidae.chars.nexus
- pythonidae.chars.phylip
- pythonidae.fasta
- pythonidae.mb.run1.t
- pythonidae.mb.run2.t
- pythonidae.mb.run3.t
- pythonidae.mb.run4.t
- pythonidae.mcmc-con.nex
- pythonidae.mcmc.nex
- pythonidae.mcmc1.nex
- pythonidae.mcmc2.nex
- pythonidae.mcmc3.nex
- pythonidae.mcmc4.nex
- pythonidae.mle.nex
- pythonidae.mle.weighted.pdm.csv
- pythonidae.nex
- pythonidae.random.bd0301.tre
- pythonidae_combined.nex
- pythonidae_continuous.chars.nexml
- pythonidae_cytb.fasta
- raxml_estimate_tree.py
- readroot.py
- readroot2.py
- remove_branch_lengths.py
- reroot_at_external_edge.py
- reroot_at_internal_edge.py
- reroot_at_midpoint.py
- reroot_at_node.py
- rescale_tree_length.py
- retain_taxa_with_labels.py
- seqgen.py
- setroot1.py
- sim_and_count_deepcoal1.py
- sim_and_count_deepcoal2.py
- splitfreq.py
- splits_on_trees.py
- symdiff1.py
- symdiff2.py
- taxa_mgmt1.py
- taxa_mgmt1a.py
- taxa_mgmt1b.py
- taxa_mgmt2.py
- taxa_mgmt3.py
- taxa_mgmt4.py
- taxa_mgmt5.py
- taxon_labels1.py
- taxon_labels2.py
- taxon_labels2b.py
- taxon_labels3.py
- taxon_labels4.py
- taxon_namespace_partition.py
- to_outgroup_position.py
- tree_clone_and_prune_vs_extract.py
- tree_copy1.py
- tree_copy2.py
- tree_evolve_char1.py
- tree_evolve_char2.py
- tree_extract1.py
- tree_extract2.py
- tree_extract3.py
- tree_extract4.py
- tree_iter1.py
- tree_iter2.py
- tree_length_crit.py
- tree_list_add1.py
- tree_list_copy1.py
- tree_list_copy2.py
- tree_list_copy3.py
- tree_list_ops1.py
- tree_list_ops2.py
- tree_rootings1.py
- treemeasures1.py
- weightedrf1.py
- basemodel.rst
- birthdeath.rst
- charmatrixmodel.rst
- charstatemodel.rst
- coalescent.rst
- continuous.rst
- datasetmodel.rst
- discrete.rst
- index.rst
- parsimony.rst
- phylogeneticdistance.rst
- popgensim.rst
- popgenstat.rst
- probability.rst
- protractedspeciation.rst
- reconcile.rst
- statistics.rst
- taxonmodel.rst
- treecollectionmodel.rst
- treecompare.rst
- treemeasure.rst
- treemodel.rst
- treescore.rst
- treeshape.rst
- treesim.rst
- bipartitions.rst
- chars.rst
- converting.rst
- dataobjects.rst
- datasets.rst
- genbank.rst
- index.rst
- paup.rst
- phylogenetic_character_analyses.rst
- phylogenetic_distances.rst
- popgenstats.rst
- raxml.rst
- reading_and_writing.rst
- seqgen.rst
- taxa.rst
- taxa_partitions.rst
- treecollections.rst
- treemanips.rst
- trees.rst
- treesims.rst
- treestats.rst
- working_with_metadata_annotations.rst
- index.rst
- sumtrees.rst
- fasta_as_string.py
- fasta_dataset_get.py
- fasta_dataset_read.py
- fasta_dnacharactermatrix_get.py
- fasta_infinitesitescharactermatrix_get.py
- fasta_proteincharactermatrix_get.py
- fasta_restrictionsitescharactermatrix_get.py
- fasta_rnacharactermatrix_get.py
- fasta_standardcharactermatrix_get.py
- fasta_write.py
- newick_as_string.py
- newick_dataset_get.py
- newick_dataset_read.py
- newick_tree_get.py
- newick_tree_get_from_path.py
- newick_tree_get_from_stream.py
- newick_treearray_read.py
- newick_treelist_get.py
- newick_treelist_read.py
- newick_write.py
- nexml_chars_as_string.py
- nexml_chars_write.py
- nexml_dataset_as_string.py
- nexml_dataset_get.py
- nexml_dataset_read.py
- nexml_dataset_write.py
- nexml_dnacharactermatrix_get.py
- nexml_infinitesitescharactermatrix_get.py
- nexml_proteincharactermatrix_get.py
- nexml_restrictionsitescharactermatrix_get.py
- nexml_rnacharactermatrix_get.py
- nexml_standardcharactermatrix_get.py
- nexml_tree_get.py
- nexml_treearray_get.py
- nexml_treearray_read.py
- nexml_treelist_get.py
- nexml_treelist_read.py
- nexml_trees_as_string.py
- nexml_trees_write.py
- nexus_chars_as_string.py
- nexus_chars_write.py
- nexus_dataset_as_string.py
- nexus_dataset_get.py
- nexus_dataset_read.py
- nexus_dataset_write.py
- nexus_dnacharactermatrix_get.py
- nexus_infinitesitescharactermatrix_get.py
- nexus_proteincharactermatrix_get.py
- nexus_restrictionsitescharactermatrix_get.py
- nexus_rnacharactermatrix_get.py
- nexus_standardcharactermatrix_get.py
- nexus_tree_get.py
- nexus_tree_get_from_path.py
- nexus_tree_get_from_stream.py
- nexus_treearray_read.py
- nexus_treelist_get.py
- nexus_treelist_read.py
- nexus_trees_as_string.py
- nexus_trees_write.py
- phylip_as_string.py
- phylip_dataset_get.py
- phylip_dataset_read.py
- phylip_dnacharactermatrix_get.py
- phylip_infinitesitescharactermatrix_get.py
- phylip_proteincharactermatrix_get.py
- phylip_restrictionsitescharactermatrix_get.py
- phylip_rnacharactermatrix_get.py
- phylip_standardcharactermatrix_get.py
- phylip_write.py
- fasta.rst
- index.rst
- newick.rst
- nexml.rst
- nexus.rst
- phylip.rst
- acknowledgements.inc
- changes.rst
- citation.inc
- code_of_conduct.rst
- conf.py
- developer.rst
- downloading.rst
- glossary.rst
- index.rst
- license.inc
- migration.rst
- news.rst
- planning.rst
- .gitignore
- make.bat
- Makefile
- netlify.toml
- requirements.in
- requirements.txt
- bibtex-tidy.sh
- paper.bib
- paper.md
- datamodel-copying-conventions.txt
- roadmap.md
- .gitignore
- __init__.py
- dendropy_format.py
- sumlabels.py
- sumtrees.py
- __init__.py
- combinatorics.py
- mathfn.py
- phylogeneticdistance.py
- popgenstat.py
- probability.py
- profiledistance.py
- statistics.py
- treecompare.py
- treemeasure.py
- treescore.py
- treesum.py
- __init__.py
- fastareader.py
- fastawriter.py
- ioservice.py
- multiphylipreader.py
- newick.py
- newickreader.py
- newickwriter.py
- newickyielder.py
- nexmlreader.py
- nexmlwriter.py
- nexmlyielder.py
- nexusprocessing.py
- nexusreader.py
- nexuswriter.py
- nexusyielder.py
- phylipreader.py
- phylipwriter.py
- tokenizer.py
- xmlprocessing.py
- __init__.py
- _bipartition.py
- _edge.py
- _node.py
- _tree.py
- __init__.py
- basemodel.py
- charmatrixmodel.py
- charstatemodel.py
- datasetmodel.py
- taxonmodel.py
- treecollectionmodel.py
- __init__.py
- ape.py
- biopython.py
- entrez.py
- ete.py
- gbif.py
- genbank.py
- itol.py
- muscle.py
- paup.py
- raxml.py
- rspr.py
- rstats.py
- seqgen.py
- __init__.py
- coalescent.py
- continuous.py
- ncbi.py
- popgensim.py
- popgenstat.py
- reconcile.py
- seqmodel.py
- seqsim.py
- treecalc.py
- treemanip.py
- treesim.py
- treesplit.py
- treesum.py
- __init__.py
- mathfn.py
- probability.py
- statistics.py
- __init__.py
- birthdeath.py
- coalescent.py
- continuous.py
- discrete.py
- multispeciescoalescent.py
- parsimony.py
- protractedspeciation.py
- reconcile.py
- treeshape.py
- __init__.py
- asciiplot.py
- tikzplot.py
- __init__.py
- charsim.py
- popgensim.py
- treesim.py
- __init__.py
- rsubprocess.R
- __init__.py
- bibtex.py
- bitprocessing.py
- cli.py
- constants.py
- container.py
- debug.py
- deprecate.py
- error.py
- filesys.py
- messaging.py
- metavar.py
- processio.py
- terminal.py
- textprocessing.py
- timeprocessing.py
- urlio.py
- vcsinfo.py
- __init__.py
- __main__.py
- __init__.py
- dendropy
- test_bibtex.py
- test_birthdeath.py
- test_charmatrixmodel.py
- test_charstatemodel.py
- test_cli.py
- test_coalescent.py
- test_combinatorics.py
- test_container.py
- test_datasetmodel.py
- test_debug.py
- test_discrete.py
- test_error.py
- test_filesys.py
- test_genbank.py
- test_mathfn.py
- test_messaging.py
- test_nexusprocessing.py
- test_parsimony.py
- test_phylipreader.py
- test_phylogeneticdistance.py
- test_popgensim.py
- test_popgenstat.py
- test_probability.py
- test_profiledistance.py
- test_reconcile.py
- test_statistics.py
- test_taxonmodel.py
- test_terminal.py
- test_textprocessing.py
- test_timeprocessing.py
- test_treecollectionmodel.py
- test_treeshape.py
- test_treesum.py
- actinopterygii.chars.nexus
- angiosperms.chars.nexus
- angiosperms.chars.txt
- apternodus.chars.hacked-for-tests.txt
- apternodus.chars.interleaved.nexus
- apternodus.chars.nexml
- apternodus.chars.nexus
- avian-ovomucoids.chars.nexus
- avian-ovomucoids.chars.txt
- bad_names.fasta
- caenophidia_mos.chars.fasta
- caenophidia_mos.chars.nexus
- caenophidia_mos.chars.txt
- cetaceans.nex
- codons.nexml
- COII_Apes.nex
- community.data.tsv
- crotaphytus_bicinctores.cytb.aligned.nexml
- crotaphytus_bicinctores.nd2.aligned.nexml
- GEBA.chars.nexus
- interleaved-charsets-all.nex
- interleaved-charsets-c1.nex
- interleaved-charsets-c2.nex
- interleaved-charsets-c3.nex
- orti.nex
- primates.chars.csv
- primates.chars.fasta
- primates.chars.interleaved.nexus
- primates.chars.nexus
- primates.chars.simple.interleaved.nexus
- primates.chars.simple.nexus
- primates.chars.subsets-1stpos.nexus
- primates.chars.subsets-2ndpos.nexus
- primates.chars.subsets-3rdpos.nexus
- primates.chars.subsets-all.nexus
- primates.chars.subsets-coding.nexus
- primates.chars.subsets-noncoding.nexus
- pythonidae.chars.beast.calibrated.xml
- pythonidae.chars.beast.uncalibrated.xml
- pythonidae.chars.fasta
- pythonidae.chars.interleaved.nexus
- pythonidae.chars.nexus
- pythonidae.chars.phylip
- pythonidae.chars.txt
- pythonidae_continuous.chars.nexml
- pythonidae_continuous.chars.nexus
- pythonidae_continuous.chars.txt
- sfs_test_single_pop_100x500_01.data.dna.fasta
- sfs_test_single_pop_100x500_01.data.std.fasta
- sfs_test_single_pop_100x500_01.sfs.folded.txt
- sfs_test_single_pop_100x500_01.sfs.unfolded.txt
- sfs_test_single_pop_100x500_02.data.dna.fasta
- sfs_test_single_pop_100x500_02.data.std.fasta
- sfs_test_single_pop_100x500_02.sfs.folded.txt
- sfs_test_single_pop_100x500_02.sfs.unfolded.txt
- sfs_test_single_pop_100x500_03.data.dna.fasta
- sfs_test_single_pop_100x500_03.data.std.fasta
- sfs_test_single_pop_100x500_03.sfs.folded.txt
- sfs_test_single_pop_100x500_03.sfs.unfolded.txt
- sfs_test_single_pop_100x500_04.data.dna.fasta
- sfs_test_single_pop_100x500_04.data.std.fasta
- sfs_test_single_pop_100x500_04.sfs.folded.txt
- sfs_test_single_pop_100x500_04.sfs.unfolded.txt
- sfs_test_single_pop_100x500_05.data.dna.fasta
- sfs_test_single_pop_100x500_05.data.std.fasta
- sfs_test_single_pop_100x500_05.sfs.folded.txt
- sfs_test_single_pop_100x500_05.sfs.unfolded.txt
- sfs_test_single_pop_100x500_06.data.dna.fasta
- sfs_test_single_pop_100x500_06.data.std.fasta
- sfs_test_single_pop_100x500_06.sfs.folded.txt
- sfs_test_single_pop_100x500_06.sfs.unfolded.txt
- sfs_test_single_pop_100x500_07.data.dna.fasta
- sfs_test_single_pop_100x500_07.data.std.fasta
- sfs_test_single_pop_100x500_07.sfs.folded.txt
- sfs_test_single_pop_100x500_07.sfs.unfolded.txt
- sfs_test_single_pop_100x500_08.data.dna.fasta
- sfs_test_single_pop_100x500_08.data.std.fasta
- sfs_test_single_pop_100x500_08.sfs.folded.txt
- sfs_test_single_pop_100x500_08.sfs.unfolded.txt
- sfs_test_single_pop_100x500_09.data.dna.fasta
- sfs_test_single_pop_100x500_09.data.std.fasta
- sfs_test_single_pop_100x500_09.sfs.folded.txt
- sfs_test_single_pop_100x500_09.sfs.unfolded.txt
- sfs_test_single_pop_100x500_10.data.dna.fasta
- sfs_test_single_pop_100x500_10.data.std.fasta
- sfs_test_single_pop_100x500_10.sfs.folded.txt
- sfs_test_single_pop_100x500_10.sfs.unfolded.txt
- sfs_test_single_pop_10x10.data.dna.fasta
- sfs_test_single_pop_10x10.data.std.fasta
- sfs_test_single_pop_10x10.sfs.folded.txt
- sfs_test_single_pop_10x10.sfs.unfolded.txt
- standard-test-chars-continuous.as_cells.nexml
- standard-test-chars-continuous.as_seqs.nexml
- standard-test-chars-continuous.interleaved.phylip
- standard-test-chars-continuous.mesquite.interleaved.nexus
- standard-test-chars-continuous.mesquite.nexus
- standard-test-chars-continuous.relaxed.phylip
- standard-test-chars-dna.as_cells.nexml
- standard-test-chars-dna.as_seqs.nexml
- standard-test-chars-dna.basic.nexus
- standard-test-chars-dna.fasta
- standard-test-chars-dna.interleaved.nexus
- standard-test-chars-dna.matchchar.nexus
- standard-test-chars-dna.multi.nexus
- standard-test-chars-dna.relaxed.phylip
- standard-test-chars-dna.simple.nexus
- standard-test-chars-generic.as_cells.nexml
- standard-test-chars-generic.as_seqs.nexml
- standard-test-chars-generic.basic.nexus
- standard-test-chars-generic.dotted.nexus
- standard-test-chars-generic.interleaved.nexus
- standard-test-chars-generic.relaxed.phylip
- standard-test-chars-generic.simple.nexus
- standard-test-chars-multiple-char-blocks.1.basic.nexus
- standard-test-chars-multiple.as_cells.nexml
- standard-test-chars-multiple.as_seqs.nexml
- standard-test-chars-protein.as_cells.nexml
- standard-test-chars-protein.as_seqs.nexml
- standard-test-chars-protein.basic.nexus
- standard-test-chars-protein.fasta
- standard-test-chars-protein.interleaved.nexus
- standard-test-chars-protein.matchchar.nexus
- standard-test-chars-protein.multi.nexus
- standard-test-chars-protein.relaxed.phylip
- standard-test-chars-protein.simple.nexus
- standard-test-chars-rna.as_cells.nexml
- standard-test-chars-rna.as_seqs.nexml
- standard-test-chars-rna.basic.nexus
- standard-test-chars-rna.fasta
- standard-test-chars-rna.interleaved.nexus
- standard-test-chars-rna.matchchar.nexus
- standard-test-chars-rna.multi.nexus
- standard-test-chars-rna.relaxed.phylip
- standard-test-chars-rna.simple.nexus
- GEBA.mixed.nexus
- geospiza.nex
- multitaxa_mesquite.nex
- reference_single_taxonset_dataset.nex
- standard-test-mixed.1.basic.nexus
- birth-death-test-data1.json
- community.data.tsv
- community.data.weighted.unnormalized.ses.mntd.csv
- community.data.weighted.unnormalized.ses.mpd.csv
- hiv1.distances.csv
- hiv1.node-to-node-dists.csv
- hiv1.unweighted.node-to-node-dists.csv
- laurasiatherian.distances.ml.csv
- multispecies_coalescent_test_data.json
- protracted_speciation_process.json
- pythonidae.mle.node-to-node-dists.csv
- pythonidae.mle.unweighted.node-to-node-dists.csv
- pythonidae.mle.unweighted.pdm.csv
- pythonidae.mle.weighted.pdm.csv
- saitou_and_nei_1987_table1.csv
- wpnjex.csv
- wpupgmaex.csv
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-False.use-tree-weights-False.burnin-0.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-False.use-tree-weights-False.burnin-150.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-False.use-tree-weights-None.burnin-0.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-False.use-tree-weights-None.burnin-150.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-False.use-tree-weights-True.burnin-0.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-False.use-tree-weights-True.burnin-150.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-None.use-tree-weights-False.burnin-0.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-None.use-tree-weights-False.burnin-150.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-None.use-tree-weights-None.burnin-0.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-None.use-tree-weights-None.burnin-150.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-None.use-tree-weights-True.burnin-0.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-None.use-tree-weights-True.burnin-150.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-True.use-tree-weights-False.burnin-0.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-True.use-tree-weights-False.burnin-150.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-True.use-tree-weights-None.burnin-0.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-True.use-tree-weights-None.burnin-150.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-True.use-tree-weights-True.burnin-0.splits.txt
- cetaceans.mb.no-clock.mcmc.trees.is-rooted-True.use-tree-weights-True.burnin-150.splits.txt
- cetaceans.mb.no-clock.mcmc.weighted-01.trees.is-rooted-False.use-tree-weights-False.burnin-0.splits.txt
- cetaceans.mb.no-clock.mcmc.weighted-01.trees.is-rooted-False.use-tree-weights-False.burnin-150.splits.txt
- cetaceans.mb.no-clock.mcmc.weighted-01.trees.is-rooted-False.use-tree-weights-None.burnin-0.splits.txt
- cetaceans.mb.no-clock.mcmc.weighted-01.trees.is-rooted-False.use-tree-weights-None.burnin-150.splits.txt
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- cetaceans.raxml.bootstraps.weighted-03.trees.is-rooted-False.use-tree-weights-True.burnin-150.splits.txt
- cetaceans.raxml.bootstraps.weighted-03.trees.is-rooted-None.use-tree-weights-False.burnin-0.splits.txt
- cetaceans.raxml.bootstraps.weighted-03.trees.is-rooted-None.use-tree-weights-False.burnin-150.splits.txt
- cetaceans.raxml.bootstraps.weighted-03.trees.is-rooted-None.use-tree-weights-None.burnin-0.splits.txt
- cetaceans.raxml.bootstraps.weighted-03.trees.is-rooted-None.use-tree-weights-None.burnin-150.splits.txt
- cetaceans.raxml.bootstraps.weighted-03.trees.is-rooted-None.use-tree-weights-True.burnin-0.splits.txt
- cetaceans.raxml.bootstraps.weighted-03.trees.is-rooted-None.use-tree-weights-True.burnin-150.splits.txt
- cetaceans.raxml.bootstraps.weighted-03.trees.is-rooted-True.use-tree-weights-False.burnin-0.splits.txt
- cetaceans.raxml.bootstraps.weighted-03.trees.is-rooted-True.use-tree-weights-False.burnin-150.splits.txt
- cetaceans.raxml.bootstraps.weighted-03.trees.is-rooted-True.use-tree-weights-None.burnin-0.splits.txt
- cetaceans.raxml.bootstraps.weighted-03.trees.is-rooted-True.use-tree-weights-None.burnin-150.splits.txt
- cetaceans.raxml.bootstraps.weighted-03.trees.is-rooted-True.use-tree-weights-True.burnin-0.splits.txt
- cetaceans.raxml.bootstraps.weighted-03.trees.is-rooted-True.use-tree-weights-True.burnin-150.splits.txt
- issue_mth_2009-02-03.rooted.nexus.is-rooted-False.use-tree-weights-False.burnin-0.splits.txt
- issue_mth_2009-02-03.rooted.nexus.is-rooted-False.use-tree-weights-None.burnin-0.splits.txt
- issue_mth_2009-02-03.rooted.nexus.is-rooted-False.use-tree-weights-True.burnin-0.splits.txt
- issue_mth_2009-02-03.rooted.nexus.is-rooted-None.use-tree-weights-False.burnin-0.splits.txt
- issue_mth_2009-02-03.rooted.nexus.is-rooted-None.use-tree-weights-None.burnin-0.splits.txt
- issue_mth_2009-02-03.rooted.nexus.is-rooted-None.use-tree-weights-True.burnin-0.splits.txt
- issue_mth_2009-02-03.rooted.nexus.is-rooted-True.use-tree-weights-False.burnin-0.splits.txt
- issue_mth_2009-02-03.rooted.nexus.is-rooted-True.use-tree-weights-None.burnin-0.splits.txt
- issue_mth_2009-02-03.rooted.nexus.is-rooted-True.use-tree-weights-True.burnin-0.splits.txt
- issue_mth_2009-02-03.unrooted.nexus.is-rooted-False.use-tree-weights-False.burnin-0.splits.txt
- issue_mth_2009-02-03.unrooted.nexus.is-rooted-False.use-tree-weights-None.burnin-0.splits.txt
- issue_mth_2009-02-03.unrooted.nexus.is-rooted-False.use-tree-weights-True.burnin-0.splits.txt
- issue_mth_2009-02-03.unrooted.nexus.is-rooted-None.use-tree-weights-False.burnin-0.splits.txt
- issue_mth_2009-02-03.unrooted.nexus.is-rooted-None.use-tree-weights-None.burnin-0.splits.txt
- issue_mth_2009-02-03.unrooted.nexus.is-rooted-None.use-tree-weights-True.burnin-0.splits.txt
- issue_mth_2009-02-03.unrooted.nexus.is-rooted-True.use-tree-weights-False.burnin-0.splits.txt
- issue_mth_2009-02-03.unrooted.nexus.is-rooted-True.use-tree-weights-None.burnin-0.splits.txt
- issue_mth_2009-02-03.unrooted.nexus.is-rooted-True.use-tree-weights-True.burnin-0.splits.txt
- APG_Angiosperms.newick
- APG_Angiosperms.nexus
- apternodus.tre
- Bininda-emonds_2007_mammals.newick
- Bininda-emonds_2007_mammals.nexus
- bipartition_encoding_fixture.json
- bird_orders.newick
- bird_orders.nex
- cetaceans.mb.no-clock.mcmc.trees
- cetaceans.mb.no-clock.mcmc.weighted-01.trees
- cetaceans.mb.no-clock.mcmc.weighted-02.trees
- cetaceans.mb.no-clock.mcmc.weighted-03.trees
- cetaceans.mb.strict-clock.mcmc.trees
- cetaceans.mb.strict-clock.mcmc.weighted-01.trees
- cetaceans.mb.strict-clock.mcmc.weighted-02.trees
- cetaceans.mb.strict-clock.mcmc.weighted-03.trees
- cetaceans.raxml.bootstraps.trees
- cetaceans.raxml.bootstraps.weighted-01.trees
- cetaceans.raxml.bootstraps.weighted-02.trees
- cetaceans.raxml.bootstraps.weighted-03.trees
- cetaceans.taxa.nex
- community.tree.newick
- curated-with-translate-block-and-internal-taxa.nex
- curated-with-translate-block-and-no-taxa-block-and-untranslated-internal-taxa.nex
- curated-with-translate-block-and-no-taxa-block.nex
- curated-with-translate-block-and-untranslated-internal-taxa.nex
- deepcoal1.nex
- dendropy-test-trees-multifurcating-rooted-annotated.json
- dendropy-test-trees-multifurcating-rooted-annotated.newick
- dendropy-test-trees-multifurcating-rooted-annotated.nexml
- dendropy-test-trees-multifurcating-rooted-annotated.nexus
- dendropy-test-trees-multifurcating-rooted-annotated.nexus-metadata-comments.json
- dendropy-test-trees-multifurcating-rooted.json
- dendropy-test-trees-multifurcating-rooted.newick
- dendropy-test-trees-multifurcating-rooted.nexml
- dendropy-test-trees-multifurcating-rooted.nexus
- dendropy-test-trees-multifurcating-unrooted.json
- dendropy-test-trees-multifurcating-unrooted.newick
- dendropy-test-trees-multifurcating-unrooted.nexml
- dendropy-test-trees-multifurcating-unrooted.nexus
- dendropy-test-trees-n10-rooted-treeshapes.json
- dendropy-test-trees-n10-rooted-treeshapes.newick
- dendropy-test-trees-n10-rooted-treeshapes.nexml
- dendropy-test-trees-n10-rooted-treeshapes.nexus
- dendropy-test-trees-n12-x2.json
- dendropy-test-trees-n12-x2.newick
- dendropy-test-trees-n12-x2.nexml
- dendropy-test-trees-n12-x2.nexus
- dendropy-test-trees-n14-unrooted-treeshapes.json
- dendropy-test-trees-n14-unrooted-treeshapes.newick
- dendropy-test-trees-n14-unrooted-treeshapes.nexml
- dendropy-test-trees-n14-unrooted-treeshapes.nexus
- dendropy-test-trees-n33-unrooted-annotated-x10a.json
- dendropy-test-trees-n33-unrooted-annotated-x10a.newick
- dendropy-test-trees-n33-unrooted-annotated-x10a.nexml
- dendropy-test-trees-n33-unrooted-annotated-x10a.nexus
- dendropy-test-trees-n33-unrooted-annotated-x10a.nexus-metadata-comments.json
- dendropy-test-trees-n33-unrooted-x100a.json
- dendropy-test-trees-n33-unrooted-x100a.newick
- dendropy-test-trees-n33-unrooted-x100a.nexml
- dendropy-test-trees-n33-unrooted-x100a.nexus
- dendropy-test-trees-n33-unrooted-x10a.json
- dendropy-test-trees-n33-unrooted-x10a.newick
- dendropy-test-trees-n33-unrooted-x10a.nexml
- dendropy-test-trees-n33-unrooted-x10a.nexus
- dendropy-test-trees-n33-unrooted-x10b.json
- dendropy-test-trees-n33-unrooted-x10b.newick
- dendropy-test-trees-n33-unrooted-x10b.nexml
- dendropy-test-trees-n33-unrooted-x10b.nexus
- feb032009.splits.csv
- feb032009.trees.newick
- feb032009.trees.nexus
- GEBA.tree.newick
- GEBA.tree.nexus
- hiv1.newick
- hiv1.nexus
- incomplete_leaves_rooted.dendropy-pruned.nex
- incomplete_leaves_rooted.paup-pruned.nex
- incomplete_leaves_rooted.pre-pruned.nex
- incomplete_leaves_rooted.pruned_taxa.txt
- incomplete_leaves_rooted.retained_taxa.txt
- incomplete_leaves_unrooted.dendropy-pruned.nex
- incomplete_leaves_unrooted.paup-pruned.nex
- incomplete_leaves_unrooted.pre-pruned.nex
- incomplete_leaves_unrooted.pruned_taxa.txt
- incomplete_leaves_unrooted.retained_taxa.txt
- issue_mth_2009-02-03.rooted.nexus
- issue_mth_2009-02-03.unrooted.nexus
- Jetz_et_al_2012_Aves.sample.tree.newick
- Jetz_et_al_2012_Aves.sample.tree.nexus
- maj-rule-bug1.trees.nexus
- maj-rule-bug2.trees.nexus
- multitreeblocks.nex
- multitreeblocks2.nex
- primates.beast.mcct.meanh.tre
- primates.beast.mcct.medianh.tre
- primates.beast.mcct.noedgelens.tree
- primates.beast.mcmc.trees
- primates.trees.nexus
- prune_rooted.dendropy-pruned.nex
- prune_rooted.paup-pruned.nex
- prune_rooted.pre-pruned.nex
- prune_rooted.pruned_taxa.txt
- prune_rooted.retained_taxa.txt
- prune_unrooted.dendropy-pruned.nex
- prune_unrooted.paup-pruned.nex
- prune_unrooted.pre-pruned.nex
- prune_unrooted.pruned_taxa.txt
- prune_unrooted.retained_taxa.txt
- pythonidae.annotated.bad.nexml
- pythonidae.annotated.nexml
- pythonidae.beast.mcmc.trees
- pythonidae.beast.summary.tre
- pythonidae.lower.mle.nex
- pythonidae.mb.con
- pythonidae.mb.run1.t
- pythonidae.mb.run2.t
- pythonidae.mb.run3.t
- pythonidae.mb.run4.t
- pythonidae.mlboots.newick.tre
- pythonidae.mlboots.nexus.tre
- pythonidae.mle.newick
- pythonidae.mle.nex
- pythonidae.mle.numbered-nodes.newick
- pythonidae.random.bd0301.midpoint-rooted.tre
- pythonidae.random.bd0301.randomly-rooted.tre
- pythonidae.random.bd0301.tre
- pythonidae.reference-trees.newick
- pythonidae.reference-trees.nexus
- pythonidae.reference-trees.no-taxa-block.nexus
- pythonidae.reference-trees.no-taxa-no-translate-block.nexus
- pythonidae.reference-trees.taxon-numbers-only.newick
- pythonidae.upper.mle.nex
- rana.trees.nexus
- Smith_2001_angiosperms.newick
- Smith_2001_angiosperms.nexus
- treebase_s373.xml
- __init__.py
- compare_and_validate.py
- coverage_analysis.py
- curated_dataset.py
- curated_test_tree.py
- curated_test_tree_list.py
- dendropytest.py
- mockrandom.py
- mockreader.py
- pathmap.py
- paupsplitsreference.py
- standard_file_test_chars.py
- standard_file_test_datasets.py
- standard_file_test_trees.py
- __init__.py
- __main__.py
- base_newick_test_cases.py
- base_standard_trees_parsing_test_cases.py
- dendropy
- test_application_sumtrees.py
- test_asciitree.py
- test_birthdeath.py
- test_coalescent.py
- test_container_frozen_ordered_dict.py
- test_container_normalized_bitmask_dict.py
- test_container_ordered_set.py
- test_continuous.py
- test_dataio_basic_tree.py
- test_dataio_fasta_reader.py
- test_dataio_fasta_writer.py
- test_dataio_newick_reader_rooting.py
- test_dataio_newick_reader_tree.py
- test_dataio_newick_reader_tree_iter.py
- test_dataio_newick_reader_tree_list.py
- test_dataio_newick_writer.py
- test_dataio_nexml_reader_chars.py
- test_dataio_nexml_reader_tree_list.py
- test_dataio_nexml_writer_chars.py
- test_dataio_nexml_writer_trees.py
- test_dataio_nexus_reader_chars.py
- test_dataio_nexus_reader_dataset.py
- test_dataio_nexus_reader_tree_list.py
- test_dataio_nexus_taxon_handling.py
- test_dataio_nexus_tree_yielder.py
- test_dataio_nexus_writer_chars.py
- test_dataio_nexus_writer_dataset.py
- test_dataio_nexus_writer_tree.py
- test_dataio_nexus_writer_tree_list.py
- test_dataio_phylip_reader_chars.py
- test_dataio_phylip_writer_chars.py
- test_dataio_tokenizer.py
- test_datamodel_annotations.py
- test_datamodel_bipartitions.py
- test_datamodel_charmatrix.py
- test_datamodel_dataset.py
- test_datamodel_split_bitmasks.py
- test_datamodel_statealphabet.py
- test_datamodel_taxon.py
- test_datamodel_tree_construction_copying_and_identity.py
- test_datamodel_tree_edge_fundamentals.py
- test_datamodel_tree_list.py
- test_datamodel_tree_node_fundamentals.py
- test_datamodel_tree_structure_and_iteration.py
- test_datamodel_tree_taxon_management.py
- test_datamodel_treearray.py
- test_discrete.py
- test_fitch.py
- test_multispeciescoalescent.py
- test_parsimony_scoring.py
- test_paup.py
- test_phylogenetic_distance_matrix.py
- test_popgenstat.py
- test_processio.py
- test_protractedspeciation.py
- test_sfs.py
- test_statistics.py
- test_tree_calculations_and_metrics.py
- test_tree_from_splits.py
- test_tree_operations_and_manipulations.py
- test_tree_reconciliation_and_discordance.py
- test_tree_shape_kernel.py
- test_tree_split_compatibility.py
- test_tree_summarization_and_consensus.py
- __init__.py
- .ctags
- .gitignore
- AUTHORS.rst
- bumpver.toml
- CHANGES.rst
- CITATION.cff
- clean.sh
- CODE_OF_CONDUCT.rst
- LICENSE.rst
- lint.sh
- MANIFEST.in
- NOTICES.rst
- pypi_release.sh
- README.md
- setup.cfg
- setup.py
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