Build.PL
data/basic.nex
data/color-my-taxsets.nex
data/Liang_et_al_Figure.nex
data/SPAN_Family3il.nex
data/SPAN_Family3il.pdf
data/SPAN_Family3il.ps
doc/buglist.txt
doc/changes.txt
doc/example1.nex
doc/Installation.pod
doc/NEXUS_coverage.html
doc/ToDo.txt
doc/Tutorial.pod
doc/UserManual.pod
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/tree_equality.pl
exec/tree_length.pl
exec/tree2nex.pl
lib/Bio/NEXUS.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/TaxaBlock.pm
lib/Bio/NEXUS/TaxUnit.pm
lib/Bio/NEXUS/TaxUnitSet.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
LICENSE
Makefile.PL
MANIFEST
META.yml			Module meta-data (added by MakeMaker)
README
README_admin
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/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/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/Bird_Ovomucoids.nex
t/data/compliant/char-interleave.nex
t/data/compliant/char-matrix-spaces.nex
t/data/compliant/characters-block-interleave.nex
t/data/compliant/data-block_clustalw.nex
t/data/compliant/dist_interleave_lower_nodiag.nex
t/data/compliant/dist_interleave_lower.nex
t/data/compliant/dist_interleave_rect_nodiag.nex
t/data/compliant/dist_interleave_upper_nodiag.nex
t/data/compliant/dist_interleave_upper.nex
t/data/compliant/dist_lower_no-diag.nex
t/data/compliant/dist_lower.nex
t/data/compliant/dist_rect.nex
t/data/compliant/dist_upper_no-diag.nex
t/data/compliant/dist_upper.nex
t/data/compliant/example1.nex
t/data/compliant/FaresWolfeCCT.nex
t/data/compliant/HCRT_all_orths_pep1_msfed1.aln.nxs
t/data/compliant/history-block_probab-distrib.nex
t/data/compliant/Human_mt_DNA.nex
t/data/compliant/intrablock-comment.nex
t/data/compliant/Kingdoms_DNA.nex
t/data/compliant/KOG0003.nex
t/data/compliant/long-names.nex
t/data/compliant/Marsupial_Wolf.nex
t/data/compliant/multiline-intrablock-comment.nex
t/data/compliant/Omland-Orioles.nex
t/data/compliant/Omland-Ravens.nex
t/data/compliant/Primate_mtDNA.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/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/temp.nex
t/data/compliant/top-level-comment.nex
t/data/compliant/tree-nhx.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/trees_branch-support-values.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/unaligned_simple_01.nex
t/data/compliant/UnaSmithHIV-both.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_quotemeta.t
t/tree_parsing.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
Build.PL
LICENSE
MANIFEST
META.yml			Module meta-data (added by MakeMaker)
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/NEXUS_coverage.html
doc/ToDo.txt
doc/Tutorial.pod
doc/UserManual.pod
doc/buglist.txt
doc/changes.txt
doc/example1.nex
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/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/_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/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
