Files

• Build.PL
• LICENSE
• MANIFEST
• META.yml
• Makefile.PL
• README
• README_admin
• data/Liang_et_al_Figure.nex
• data/SPAN_Family3il.nex
• data/SPAN_Family3il.pdf
• data/SPAN_Family3il.ps
• data/basic.nex
• data/color-my-taxsets.nex
• doc/._Installation.pod
• doc/._ToDo.txt
• doc/._Tutorial.pod
• doc/._changes.txt
• doc/Installation.pod
• doc/NEXUS_coverage.html
• doc/ToDo.txt
• doc/Tutorial.pod
• doc/UserManual.pod
• doc/buglist.txt
• doc/changes.txt
• doc/example1.nex
• exec/._tree_length.pl
• exec/align2nex.pl
• exec/bugs.cmd.pl
• exec/bugs.pl
• exec/extract_taxset.pl
• exec/history.pl
• exec/jags.pl
• exec/newtonex.pl
• exec/nex2text_tree.pl
• exec/nexdiff.pl
• exec/nexdump.pl
• exec/nexfix.pl
• exec/nexplot.pl
• exec/nextool.pl
• exec/nexus-convert.pl
• exec/p3treeplot.pl
• exec/pppplot.pl
• exec/readin_tcoffee.pl
• exec/roundtrip.pl
• exec/setmaker.pl
• exec/tree2nex.pl
• exec/tree_equality.pl
• exec/tree_length.pl
• lib/Bio/NEXUS.pm
• lib/Bio/NEXUS/._UnalignedBlock.pm
• lib/Bio/NEXUS/AssumptionsBlock.pm
• lib/Bio/NEXUS/Block.pm
• lib/Bio/NEXUS/CharactersBlock.pm
• lib/Bio/NEXUS/CodonsBlock.pm
• lib/Bio/NEXUS/DataBlock.pm
• lib/Bio/NEXUS/DistancesBlock.pm
• lib/Bio/NEXUS/Functions.pm
• lib/Bio/NEXUS/HistoryBlock.pm
• lib/Bio/NEXUS/Matrix.pm
• lib/Bio/NEXUS/NHXCmd.pm
• lib/Bio/NEXUS/Node.pm
• lib/Bio/NEXUS/NotesBlock.pm
• lib/Bio/NEXUS/SetsBlock.pm
• lib/Bio/NEXUS/SpanBlock.pm
• lib/Bio/NEXUS/TaxUnit.pm
• lib/Bio/NEXUS/TaxUnitSet.pm
• lib/Bio/NEXUS/TaxaBlock.pm
• lib/Bio/NEXUS/Tools/GraphicsParams.pm
• lib/Bio/NEXUS/Tools/NexModifier.pm
• lib/Bio/NEXUS/Tools/NexPlott.swp
• lib/Bio/NEXUS/Tools/NexPlotter.pm
• lib/Bio/NEXUS/Tree.pm
• lib/Bio/NEXUS/TreesBlock.pm
• lib/Bio/NEXUS/UnalignedBlock.pm
• lib/Bio/NEXUS/UnknownBlock.pm
• lib/Bio/NEXUS/Util/Exceptions.pm
• lib/Bio/NEXUS/Util/Logger.pm
• lib/Bio/NEXUS/WeightSet.pm
• t/._notesblock_methods.t
• t/._tree_parsing.t
• t/_perl_module-loading.t
• t/_perl_perlpod.t
• t/_perl_podcoverage.t
• t/assumptionsblock_options.t
• t/assumptionsblock_wtset-scores.t
• t/block_link-and-title.t
• t/charactersblock_methods-01.t
• t/charactersblock_methods-02.t
• t/command_unknown_exception.t
• t/data/compliant/._02_character-polymorphic-uncertain.nex
• t/data/compliant/._04_characterstatelabels_05.nex
• t/data/compliant/._characters-block-interleave2.nex
• t/data/compliant/._example1.nex
• t/data/compliant/01_basic.nex
• t/data/compliant/01_taxa-labels-squarebrackets.nex
• t/data/compliant/02_assumptions-block_options_01.nex
• t/data/compliant/02_assumptions-block_options_02.nex
• t/data/compliant/02_character-polymorphic-doublequotes.nex
• t/data/compliant/02_character-polymorphic-uncertain.nex
• t/data/compliant/02_character-polymorphic.nex
• t/data/compliant/02_character-state-frequency.nex
• t/data/compliant/02_character-uncertain.nex
• t/data/compliant/02_characters-block_format_01.nex
• t/data/compliant/02_characters-block_format_02.nex
• t/data/compliant/02_characters-block_initial.nex
• t/data/compliant/02_notes-text.nex
• t/data/compliant/02_wtset-scores.nex
• t/data/compliant/04_block_level_methods.nex
• t/data/compliant/04_charactersblock_methods_01.nex
• t/data/compliant/04_charactersblock_methods_02.nex
• t/data/compliant/04_charactersblock_methods_03.nex
• t/data/compliant/04_charactersblock_methods_04.nex
• t/data/compliant/04_charactersblock_methods_05.nex
• t/data/compliant/04_characterstatelabels_05.nex
• t/data/compliant/04_equals_methods.nex
• t/data/compliant/04_object-file-equality_01.nex
• t/data/compliant/04_object-file-equality_02.nex
• t/data/compliant/04_private-commands.nex
• t/data/compliant/04_shared_commands_01.nex
• t/data/compliant/04_shared_commands_02.nex
• t/data/compliant/04_shared_commands_03.nex
• t/data/compliant/04_shared_commands_04.nex
• t/data/compliant/04_shared_commands_05.nex
• t/data/compliant/Bird_Ovomucoids.nex
• t/data/compliant/FaresWolfeCCT.nex
• t/data/compliant/HCRT_all_orths_pep1_msfed1.aln.nxs
• t/data/compliant/Human_mt_DNA.nex
• t/data/compliant/KOG0003.nex
• t/data/compliant/Kingdoms_DNA.nex
• t/data/compliant/Marsupial_Wolf.nex
• t/data/compliant/Omland-Orioles.nex
• t/data/compliant/Omland-Ravens.nex
• t/data/compliant/Primate_mtDNA.nex
• t/data/compliant/SPAN_Family10i.nex
• t/data/compliant/SPAN_Family1nlw.nex
• t/data/compliant/SPAN_Family2alw.nex
• t/data/compliant/SPAN_Family3il.nex
• t/data/compliant/SPAN_Family4nl.nex
• t/data/compliant/SPAN_Family5alw.nex
• t/data/compliant/SPAN_Family6iw.nex
• t/data/compliant/SPAN_Family7n.nex
• t/data/compliant/SPAN_Family8a.nex
• t/data/compliant/SPAN_Family9iw.nex
• t/data/compliant/Treebase-chlamy-dna.nex
• t/data/compliant/Treebase-horsetails-classic.nex
• t/data/compliant/Treebase-horsetails-dna.nex
• t/data/compliant/Treebase-liverwort-rbcl.nex
• t/data/compliant/UnaSmithHIV-both.nex
• t/data/compliant/barns-combined.nex
• t/data/compliant/basic-bush-dos.nex
• t/data/compliant/basic-bush-mac.nex
• t/data/compliant/basic-bush-unix.nex
• t/data/compliant/basic-bush.nex
• t/data/compliant/basic-ladder.nex
• t/data/compliant/basic-rake.nex
• t/data/compliant/basic-trees.nex
• t/data/compliant/char-interleave.nex
• t/data/compliant/char-matrix-spaces.nex
• t/data/compliant/characters-block-interleave.nex
• t/data/compliant/characters-block-interleave2.nex
• t/data/compliant/data-block_clustalw.nex
• t/data/compliant/dist_interleave_lower.nex
• t/data/compliant/dist_interleave_lower_nodiag.nex
• t/data/compliant/dist_interleave_rect_nodiag.nex
• t/data/compliant/dist_interleave_upper.nex
• t/data/compliant/dist_interleave_upper_nodiag.nex
• t/data/compliant/dist_lower.nex
• t/data/compliant/dist_lower_no-diag.nex
• t/data/compliant/dist_rect.nex
• t/data/compliant/dist_upper.nex
• t/data/compliant/dist_upper_no-diag.nex
• t/data/compliant/example1.nex
• t/data/compliant/history-block_probab-distrib.nex
• t/data/compliant/intrablock-comment.nex
• t/data/compliant/long-names.nex
• t/data/compliant/multiline-intrablock-comment.nex
• t/data/compliant/quoted-strings1.nex
• t/data/compliant/quoted-strings2.nex
• t/data/compliant/radical-whitespace.nex
• t/data/compliant/really-long-names.nex
• t/data/compliant/simple_taxa_and_chars.nex
• t/data/compliant/temp.nex
• t/data/compliant/top-level-comment.nex
• t/data/compliant/tree-nhx.nex
• t/data/compliant/trees-translate.nex
• t/data/compliant/trees-tree-basal-trifurcation.nex
• t/data/compliant/trees-tree-bush-branchlength-negative.nex
• t/data/compliant/trees-tree-bush-branchlength-scientific.nex
• t/data/compliant/trees-tree-bush-branchlength-zero.nex
• t/data/compliant/trees-tree-bush-cladogram.nex
• t/data/compliant/trees-tree-bush-extended-root-branch.nex
• t/data/compliant/trees-tree-bush-inode-labels-partial.nex
• t/data/compliant/trees-tree-bush-inode-labels-quoted1.nex
• t/data/compliant/trees-tree-bush-inode-labels-quoted2.nex
• t/data/compliant/trees-tree-bush-inode-labels.nex
• t/data/compliant/trees-tree-bush-quoted-string-name1.nex
• t/data/compliant/trees-tree-bush-quoted-string-name2.nex
• t/data/compliant/trees-tree-bush-uneven.nex
• t/data/compliant/trees-tree-bush.nex
• t/data/compliant/trees-tree-ladder-cladogram.nex
• t/data/compliant/trees-tree-ladder-uneven.nex
• t/data/compliant/trees-tree-ladder.nex
• t/data/compliant/trees-tree-multiple-challenges.nex
• t/data/compliant/trees-tree-multiple.nex
• t/data/compliant/trees-tree-rake-cladogram.nex
• t/data/compliant/trees-tree-rake.nex
• t/data/compliant/trees_branch-support-values.nex
• t/data/compliant/unaligned_simple_01.nex
• t/matrix_character-state-frequency.t
• t/matrix_charactersblock-interleave.t
• t/matrix_historyblock-probab-distrib.t
• t/matrix_polymorphic-and-uncertain.t
• t/nexus_add-otu-clone.t
• t/nexus_block-level-commands.t
• t/nexus_taxa-labels-quoted.t
• t/nexus_taxa-labels-squarebrackets.t
• t/nexus_taxa-labels.t
• t/nexus_wrong_format.t
• t/nhxcmd_parsing.t
• t/notesblock_methods.t
• t/tree_equals.t
• t/tree_methods-01.t
• t/tree_methods-02.t
• t/tree_parsing.t
• t/tree_parsing_quotemeta.t
• t/tree_support-values.t
• t/treesblock_methods.t
• t/uncat_clone_methods.t
• t/uncat_datablock_clustalw.t
• t/uncat_equals_methods.t
• t/uncat_excessive_whitespace.t
• t/uncat_ntax-nchar-dimensions.t
• t/uncat_object-file-equality.t
• t/uncat_shared-commands.t
• t/uncat_todo.t
• t/uncat_write.t