AUTHORS.txt
CHANGES.txt
FAQ.txt
INSTALL.txt
LICENSE.txt
MANIFEST.in
README.txt
THANKS.txt
TODO.txt
clean.sh
ez_setup.py
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
dendropy/__init__.py
dendropy/coalescent.py
dendropy/continuous.py
dendropy/popgensim.py
dendropy/popgenstat.py
dendropy/reconcile.py
dendropy/scm.py
dendropy/seqmodel.py
dendropy/seqsim.py
dendropy/treecalc.py
dendropy/treemanip.py
dendropy/treesim.py
dendropy/treesplit.py
dendropy/treesum.py
dendropy/dataio/__init__.py
dendropy/dataio/beast.py
dendropy/dataio/dataschema.py
dendropy/dataio/fasta.py
dendropy/dataio/ioclient.py
dendropy/dataio/newick.py
dendropy/dataio/nexml.py
dendropy/dataio/nexusreader_ncl.py
dendropy/dataio/nexusreader_py.py
dendropy/dataio/nexustokenizer.py
dendropy/dataio/nexustreeiter.py
dendropy/dataio/nexuswriter.py
dendropy/dataio/phylip.py
dendropy/dataio/xmlparser.py
dendropy/dataobject/__init__.py
dendropy/dataobject/base.py
dendropy/dataobject/char.py
dendropy/dataobject/dataset.py
dendropy/dataobject/taxon.py
dendropy/dataobject/tree.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/ncbi.py
dendropy/interop/paup.py
dendropy/interop/raxml.py
dendropy/interop/seqgen.py
dendropy/mathlib/__init__.py
dendropy/mathlib/distance.py
dendropy/mathlib/linearalg.py
dendropy/mathlib/mathfn.py
dendropy/mathlib/probability.py
dendropy/mathlib/statistics.py
dendropy/test/__init__.py
dendropy/test/test_annotations.py
dendropy/test/test_ape.py
dendropy/test/test_asciitree.py
dendropy/test/test_biopython.py
dendropy/test/test_coalescent.py
dendropy/test/test_containers.py
dendropy/test/test_continuous.py
dendropy/test/test_datagen.py
dendropy/test/test_dataio_beast.py
dendropy/test/test_dataio_fasta.py
dendropy/test/test_dataio_indexing.py
dendropy/test/test_dataio_newick.py
dendropy/test/test_dataio_nexml.py
dendropy/test/test_dataio_nexus.py
dendropy/test/test_dataio_nexustokenizer.py
dendropy/test/test_dataio_phylip.py
dendropy/test/test_dataio_tree_rooting.py
dendropy/test/test_dataobject_char_array.py
dendropy/test/test_dataobject_cloning.py
dendropy/test/test_dataobject_dataset.py
dendropy/test/test_dataobject_taxon.py
dendropy/test/test_dataobject_tree.py
dendropy/test/test_dataobject_tree_list.py
dendropy/test/test_distance.py
dendropy/test/test_ete.py
dendropy/test/test_fitch.py
dendropy/test/test_linearalg.py
dendropy/test/test_num_lineages_through_time.py
dendropy/test/test_paup.py
dendropy/test/test_popgensim.py
dendropy/test/test_popgenstat.py
dendropy/test/test_reconcile.py
dendropy/test/test_scm.py
dendropy/test/test_seqsim.py
dendropy/test/test_split_counting.py
dendropy/test/test_split_masking.py
dendropy/test/test_splits_on_incomplete_leaf_sets.py
dendropy/test/test_statistics.py
dendropy/test/test_sumtrees.py
dendropy/test/test_tree_calcs.py
dendropy/test/test_tree_from_splits.py
dendropy/test/test_tree_manips.py
dendropy/test/test_tree_metrics.py
dendropy/test/test_tree_sims.py
dendropy/test/test_tree_structuring.py
dendropy/test/test_tree_sums.py
dendropy/test/test_tree_taxa.py
dendropy/test/test_tree_traversal.py
dendropy/test/test_tree_truncation.py
dendropy/test/data/chars/COII_Apes.nex
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/codons.nexml
dendropy/test/data/chars/crotaphytus_bicinctores.cytb.aligned.nexml
dendropy/test/data/chars/crotaphytus_bicinctores.nd2.aligned.nexml
dendropy/test/data/chars/interleaved-charsets-all.nex
dendropy/test/data/chars/interleaved-charsets-c1.nex
dendropy/test/data/chars/interleaved-charsets-c2.nex
dendropy/test/data/chars/interleaved-charsets-c3.nex
dendropy/test/data/chars/orti.nex
dendropy/test/data/chars/primates.chars.csv
dendropy/test/data/chars/primates.chars.fasta
dendropy/test/data/chars/primates.chars.interleaved.nexus
dendropy/test/data/chars/primates.chars.nexus
dendropy/test/data/chars/primates.chars.simple.interleaved.nexus
dendropy/test/data/chars/primates.chars.simple.nexus
dendropy/test/data/chars/primates.chars.subsets-1stpos.nexus
dendropy/test/data/chars/primates.chars.subsets-2ndpos.nexus
dendropy/test/data/chars/primates.chars.subsets-3rdpos.nexus
dendropy/test/data/chars/primates.chars.subsets-all.nexus
dendropy/test/data/chars/primates.chars.subsets-coding.nexus
dendropy/test/data/chars/primates.chars.subsets-noncoding.nexus
dendropy/test/data/chars/pythonidae.chars.beast.calibrated.xml
dendropy/test/data/chars/pythonidae.chars.beast.uncalibrated.xml
dendropy/test/data/chars/pythonidae.chars.fasta
dendropy/test/data/chars/pythonidae.chars.interleaved.nexus
dendropy/test/data/chars/pythonidae.chars.nexus
dendropy/test/data/chars/pythonidae.chars.phylip
dendropy/test/data/chars/pythonidae.chars.txt
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/mixed/geospiza.nex
dendropy/test/data/mixed/multitaxa_mesquite.nex
dendropy/test/data/mixed/reference_single_taxonset_dataset.nex
dendropy/test/data/trees/apternodus.tre
dendropy/test/data/trees/bird_orders.nex
dendropy/test/data/trees/deepcoal1.nex
dendropy/test/data/trees/feb032009.splits.csv
dendropy/test/data/trees/feb032009.trees.nexus
dendropy/test/data/trees/hiv1.newick
dendropy/test/data/trees/hiv1.nexus
dendropy/test/data/trees/incomplete_leaves_rooted.dendropy-pruned.nex
dendropy/test/data/trees/incomplete_leaves_rooted.paup-pruned.nex
dendropy/test/data/trees/incomplete_leaves_rooted.pre-pruned.nex
dendropy/test/data/trees/incomplete_leaves_rooted.pruned_taxa.txt
dendropy/test/data/trees/incomplete_leaves_rooted.retained_taxa.txt
dendropy/test/data/trees/incomplete_leaves_unrooted.dendropy-pruned.nex
dendropy/test/data/trees/incomplete_leaves_unrooted.paup-pruned.nex
dendropy/test/data/trees/incomplete_leaves_unrooted.pre-pruned.nex
dendropy/test/data/trees/incomplete_leaves_unrooted.pruned_taxa.txt
dendropy/test/data/trees/incomplete_leaves_unrooted.retained_taxa.txt
dendropy/test/data/trees/maj-rule-bug1.trees.nexus
dendropy/test/data/trees/maj-rule-bug2.trees.nexus
dendropy/test/data/trees/primates.beast.mcct.meanh.tre
dendropy/test/data/trees/primates.beast.mcct.medianh.tre
dendropy/test/data/trees/primates.beast.mcct.noedgelens.tree
dendropy/test/data/trees/primates.beast.mcmc.trees
dendropy/test/data/trees/primates.trees.nexus
dendropy/test/data/trees/prune_rooted.dendropy-pruned.nex
dendropy/test/data/trees/prune_rooted.paup-pruned.nex
dendropy/test/data/trees/prune_rooted.pre-pruned.nex
dendropy/test/data/trees/prune_rooted.pruned_taxa.txt
dendropy/test/data/trees/prune_rooted.retained_taxa.txt
dendropy/test/data/trees/prune_unrooted.dendropy-pruned.nex
dendropy/test/data/trees/prune_unrooted.paup-pruned.nex
dendropy/test/data/trees/prune_unrooted.pre-pruned.nex
dendropy/test/data/trees/prune_unrooted.pruned_taxa.txt
dendropy/test/data/trees/prune_unrooted.retained_taxa.txt
dendropy/test/data/trees/pythonidae.annotated.bad.nexml
dendropy/test/data/trees/pythonidae.annotated.nexml
dendropy/test/data/trees/pythonidae.beast.mcmc.trees
dendropy/test/data/trees/pythonidae.beast.summary.tre
dendropy/test/data/trees/pythonidae.mb.con
dendropy/test/data/trees/pythonidae.mb.run1.t
dendropy/test/data/trees/pythonidae.mb.run2.t
dendropy/test/data/trees/pythonidae.mb.run3.t
dendropy/test/data/trees/pythonidae.mb.run4.t
dendropy/test/data/trees/pythonidae.mlboots.newick.tre
dendropy/test/data/trees/pythonidae.mlboots.nexus.tre
dendropy/test/data/trees/pythonidae.mle.newick
dendropy/test/data/trees/pythonidae.mle.nex
dendropy/test/data/trees/pythonidae.random.bd0301.midpoint-rooted.tre
dendropy/test/data/trees/pythonidae.random.bd0301.randomly-rooted.tre
dendropy/test/data/trees/pythonidae.random.bd0301.tre
dendropy/test/data/trees/pythonidae.reference-trees.newick
dendropy/test/data/trees/pythonidae.reference-trees.nexus
dendropy/test/data/trees/pythonidae.reference-trees.no-taxa-block.nexus
dendropy/test/data/trees/pythonidae.reference-trees.no-taxa-no-translate-block.nexus
dendropy/test/data/trees/rana.trees.nexus
dendropy/test/data/trees/treebase_s373.xml
dendropy/test/support/__init__.py
dendropy/test/support/coverage_analysis.py
dendropy/test/support/datagen.py
dendropy/test/support/datatest.py
dendropy/test/support/extendedtest.py
dendropy/test/support/generate_pruned_trees.py
dendropy/test/support/generate_reference_tree.py
dendropy/test/support/nexmlvalidator.py
dendropy/test/support/pathmap.py
dendropy/test/support/runlevel.py
dendropy/test/support/tree_parse_speed.py
dendropy/utility/ElementTree.py
dendropy/utility/__init__.py
dendropy/utility/bibtex.py
dendropy/utility/cli.py
dendropy/utility/containers.py
dendropy/utility/debugging.py
dendropy/utility/error.py
dendropy/utility/fileutils.py
dendropy/utility/iosys.py
dendropy/utility/messaging.py
dendropy/utility/session.py
dendropy/utility/termutils.py
dendropy/utility/textutils.py
dendropy/utility/vcsinfo.py
doc/Makefile
doc/source/acknowledgements.inc
doc/source/changes.rst
doc/source/conf.py
doc/source/downloading.rst
doc/source/index.rst
doc/source/license.inc
doc/source/_static/dendropy.css
doc/source/_static/dendropy.png
doc/source/_static/google-groups-logo1.png
doc/source/_static/logo_cipres.gif
doc/source/_static/nsf.gif
doc/source/_templates/layout.html
doc/source/examples/bdtree_multi1.py
doc/source/examples/bdtree_multi2.py
doc/source/examples/bibtex_annotations1.py
doc/source/examples/bibtex_annotations2.py
doc/source/examples/bibtex_annotations3.py
doc/source/examples/contained_coalescent1.py
doc/source/examples/contained_coalescent2.py
doc/source/examples/dsrw1.py
doc/source/examples/dynamic_annotations1.py
doc/source/examples/find_taxon_node1.py
doc/source/examples/find_taxon_node2.py
doc/source/examples/ladderize.py
doc/source/examples/majrule.py
doc/source/examples/mrca.py
doc/source/examples/node_ages1.py
doc/source/examples/orti1994.nex
doc/source/examples/paup_estimate_model.py
doc/source/examples/paup_estimate_tree_ml.py
doc/source/examples/paup_estimate_tree_nj.py
doc/source/examples/pbhg.py
doc/source/examples/pdm.py
doc/source/examples/pgstats1.py
doc/source/examples/pic1.py
doc/source/examples/pic_annotated.py
doc/source/examples/preorder_filtered_edge_iteration.py
doc/source/examples/preorder_filtered_node_iteration.py
doc/source/examples/primates.cc.nex
doc/source/examples/primates.cc.tre
doc/source/examples/prune_taxa_with_labels.py
doc/source/examples/pure_kingman1.py
doc/source/examples/pythonidae.beast-mcmc.trees
doc/source/examples/pythonidae.fasta
doc/source/examples/pythonidae.mb.run1.t
doc/source/examples/pythonidae.mb.run2.t
doc/source/examples/pythonidae.mb.run3.t
doc/source/examples/pythonidae.mb.run4.t
doc/source/examples/pythonidae.mcmc-con.nex
doc/source/examples/pythonidae.mcmc.nex
doc/source/examples/pythonidae.mle.nex
doc/source/examples/pythonidae.nex
doc/source/examples/pythonidae.random.bd0301.tre
doc/source/examples/raxml_estimate_tree.py
doc/source/examples/remove_branch_lengths.py
doc/source/examples/reroot_at_external_edge.py
doc/source/examples/reroot_at_internal_edge.py
doc/source/examples/reroot_at_midpoint.py
doc/source/examples/reroot_at_node.py
doc/source/examples/rescale_tree_length.py
doc/source/examples/retain_taxa_with_labels.py
doc/source/examples/seqgen.py
doc/source/examples/sim_and_count_deepcoal1.py
doc/source/examples/sim_and_count_deepcoal2.py
doc/source/examples/skel_dataio_fasta_reading.py
doc/source/examples/skel_dataio_fasta_writing.py
doc/source/examples/skel_dataio_newick_writing.py
doc/source/examples/skel_dataio_nexus_reading.py
doc/source/examples/skel_dataio_nexus_writing.py
doc/source/examples/skel_dataio_phylip_reading.py
doc/source/examples/skel_dataio_phylip_writing.py
doc/source/examples/splitfreq.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_evolve_char1.py
doc/source/examples/tree_evolve_char2.py
doc/source/examples/tree_iter1.py
doc/source/examples/tree_iter2.py
doc/source/examples/tree_length_crit.py
doc/source/examples/tree_rootings1.py
doc/source/library/base.rst
doc/source/library/char.rst
doc/source/library/coalescent.rst
doc/source/library/continuous.rst
doc/source/library/dataset.rst
doc/source/library/genbank.rst
doc/source/library/index.rst
doc/source/library/reconcile.rst
doc/source/library/taxon.rst
doc/source/library/tree.rst
doc/source/library/treecalc.rst
doc/source/library/treemanip.rst
doc/source/library/treesim.rst
doc/source/scripts/sumtrees.rst
doc/source/tutorial/changes.rst
doc/source/tutorial/chars.rst
doc/source/tutorial/converting.rst
doc/source/tutorial/dataobjects.rst
doc/source/tutorial/datasets.rst
doc/source/tutorial/examining.rst
doc/source/tutorial/genbank.rst
doc/source/tutorial/index.rst
doc/source/tutorial/interoperability.rst
doc/source/tutorial/ncbi.rst
doc/source/tutorial/paup.rst
doc/source/tutorial/phylogenetic_character_analyses.rst
doc/source/tutorial/phylogenetic_data_overview.rst
doc/source/tutorial/popgenstats.rst
doc/source/tutorial/raxml.rst
doc/source/tutorial/reading.rst
doc/source/tutorial/seqgen.rst
doc/source/tutorial/taxa.rst
doc/source/tutorial/taxa_partitions.rst
doc/source/tutorial/treemanips.rst
doc/source/tutorial/treenav.rst
doc/source/tutorial/trees.rst
doc/source/tutorial/treesims.rst
doc/source/tutorial/treestats.rst
doc/source/tutorial/working_with_characters.rst
doc/source/tutorial/working_with_datasets.rst
doc/source/tutorial/working_with_metadata_annotations.rst
doc/source/tutorial/working_with_taxa.rst
doc/source/tutorial/working_with_trees.rst
doc/source/tutorial/writing.rst
extras/README
extras/dot_dendropy/logging_dendropy.conf
extras/dot_dendropy/logging_dendropy.confdb
extras/dot_dendropy/startup.py
extras/garli_confs/add_garli.conf
extras/garli_confs/boot_add_garli.conf
extras/garli_confs/neighborhood_garli1.conf
extras/garli_confs/score_garli.conf
extras/geodispersal/LiebermanEBasidechenella.nex
extras/geodispersal/LiebermanECrassiproetus.nex
extras/geodispersal/Readme.txt
extras/geodispersal/biogeoexample.nex
extras/geodispersal/geodispersal-analysis.py
extras/geodispersal/labels.txt
extras/scripts/add_end.sh
extras/scripts/boot_mle_to_R_input.py
extras/scripts/create_paup_majrule.sh
extras/scripts/extract_and_join_paup_splits_table
extras/scripts/garli_log_to_R_input.py
extras/scripts/plot_boot_mle.R
extras/scripts/plot_time_series.R
extras/scripts/rell_from_paupsite_and_wts.py
extras/scripts/use_rell_indices_to_resampled.py
extras/scripts/verbose_to_iter_table.py
scripts/calculators/calc_pybus_harvey_gamma.py
scripts/calculators/coalign-muscle.py
scripts/calculators/extract-coalescent-frames.py
scripts/calculators/long_branch_symmdiff.py
scripts/calculators/prob-coal-tree.py
scripts/calculators/raxml-map-bipartitions.py
scripts/calculators/rtreeoutgroup.py
scripts/calculators/scale_trees.py
scripts/calculators/strict_consensus_merge.py
scripts/calculators/symmdiff_by_split_cutoff.py
scripts/calculators/treedepth.py
scripts/converters/beast-to-nexus.py
scripts/converters/fasta-to-nexus.py
scripts/converters/gbfasta.py
scripts/converters/nexus-to-nexml.py
scripts/igarli/igarli_add_tree.py
scripts/igarli/igarli_boot_add_tree.py
scripts/igarli/igarli_boot_master.py
scripts/igarli/igarli_boot_one_round.sh
scripts/igarli/igarli_master.py
scripts/igarli/igarli_neighborhood.py
scripts/igarli/igarli_one_round.sh
scripts/igarli/igarli_select_trees.py
scripts/igarli/incr_garli.py
scripts/parsers/dendropy-parse-check.py
scripts/prob_synapomorphy/prob_synapo.py
scripts/simulation/simulate-tree.py
scripts/sumtrees/cattrees.py
scripts/sumtrees/sumlabels.py
scripts/sumtrees/sumtrees.py