Files

• COPYING
• LICENSE
• MANIFEST
• META.json
• META.yml
• Makefile.PL
• README.md
• lib/Bio/Phylo.pm
• lib/Bio/Phylo/EvolutionaryModels.pm
• lib/Bio/Phylo/Factory.pm
• lib/Bio/Phylo/Forest.pm
• lib/Bio/Phylo/Forest/DrawNodeRole.pm
• lib/Bio/Phylo/Forest/DrawTreeRole.pm
• lib/Bio/Phylo/Forest/Node.pm
• lib/Bio/Phylo/Forest/NodeRole.pm
• lib/Bio/Phylo/Forest/Tree.pm
• lib/Bio/Phylo/Forest/TreeRole.pm
• lib/Bio/Phylo/Generator.pm
• lib/Bio/Phylo/IO.pm
• lib/Bio/Phylo/Identifiable.pm
• lib/Bio/Phylo/Listable.pm
• lib/Bio/Phylo/ListableRole.pm
• lib/Bio/Phylo/Manual.pod
• lib/Bio/Phylo/Matrices.pm
• lib/Bio/Phylo/Matrices/Character.pm
• lib/Bio/Phylo/Matrices/Characters.pm
• lib/Bio/Phylo/Matrices/Datatype.pm
• lib/Bio/Phylo/Matrices/Datatype/Continuous.pm
• lib/Bio/Phylo/Matrices/Datatype/Custom.pm
• lib/Bio/Phylo/Matrices/Datatype/Dna.pm
• lib/Bio/Phylo/Matrices/Datatype/Illumina.pm
• lib/Bio/Phylo/Matrices/Datatype/Mixed.pm
• lib/Bio/Phylo/Matrices/Datatype/Protein.pm
• lib/Bio/Phylo/Matrices/Datatype/Restriction.pm
• lib/Bio/Phylo/Matrices/Datatype/Rna.pm
• lib/Bio/Phylo/Matrices/Datatype/Sanger.pm
• lib/Bio/Phylo/Matrices/Datatype/Solexa.pm
• lib/Bio/Phylo/Matrices/Datatype/Standard.pm
• lib/Bio/Phylo/Matrices/Datum.pm
• lib/Bio/Phylo/Matrices/DatumRole.pm
• lib/Bio/Phylo/Matrices/Matrix.pm
• lib/Bio/Phylo/Matrices/MatrixRole.pm
• lib/Bio/Phylo/Matrices/TypeSafeData.pm
• lib/Bio/Phylo/Mediators/TaxaMediator.pm
• lib/Bio/Phylo/Models/Substitution/Binary.pm
• lib/Bio/Phylo/Models/Substitution/Dna.pm
• lib/Bio/Phylo/Models/Substitution/Dna/F81.pm
• lib/Bio/Phylo/Models/Substitution/Dna/GTR.pm
• lib/Bio/Phylo/Models/Substitution/Dna/HKY85.pm
• lib/Bio/Phylo/Models/Substitution/Dna/JC69.pm
• lib/Bio/Phylo/Models/Substitution/Dna/K80.pm
• lib/Bio/Phylo/NeXML/DOM.pm
• lib/Bio/Phylo/NeXML/DOM/Document.pm
• lib/Bio/Phylo/NeXML/DOM/Document/Libxml.pm
• lib/Bio/Phylo/NeXML/DOM/Document/Twig.pm
• lib/Bio/Phylo/NeXML/DOM/Element.pm
• lib/Bio/Phylo/NeXML/DOM/Element/Libxml.pm
• lib/Bio/Phylo/NeXML/DOM/Element/Twig.pm
• lib/Bio/Phylo/NeXML/Entities.pm
• lib/Bio/Phylo/NeXML/Meta.pm
• lib/Bio/Phylo/NeXML/Meta/XMLLiteral.pm
• lib/Bio/Phylo/NeXML/Writable.pm
• lib/Bio/Phylo/NeXML/XML2JSON.pm
• lib/Bio/Phylo/Parsers/Abstract.pm
• lib/Bio/Phylo/Parsers/Adjacency.pm
• lib/Bio/Phylo/Parsers/Cdao.pm
• lib/Bio/Phylo/Parsers/Dwca.pm
• lib/Bio/Phylo/Parsers/Fasta.pm
• lib/Bio/Phylo/Parsers/Fastq.pm
• lib/Bio/Phylo/Parsers/Figtree.pm
• lib/Bio/Phylo/Parsers/Json.pm
• lib/Bio/Phylo/Parsers/Newick.pm
• lib/Bio/Phylo/Parsers/Nexml.pm
• lib/Bio/Phylo/Parsers/Nexus.pm
• lib/Bio/Phylo/Parsers/Nhx.pm
• lib/Bio/Phylo/Parsers/Phylip.pm
• lib/Bio/Phylo/Parsers/Phyloxml.pm
• lib/Bio/Phylo/Parsers/Table.pm
• lib/Bio/Phylo/Parsers/Taxlist.pm
• lib/Bio/Phylo/Parsers/Tnrs.pm
• lib/Bio/Phylo/Parsers/Tolweb.pm
• lib/Bio/Phylo/Parsers/Ubiocbmeta.pm
• lib/Bio/Phylo/Parsers/Ubiometa.pm
• lib/Bio/Phylo/Parsers/Ubiosearch.pm
• lib/Bio/Phylo/PhyloWS.pm
• lib/Bio/Phylo/PhyloWS/Client.pm
• lib/Bio/Phylo/PhyloWS/Resource.pm
• lib/Bio/Phylo/PhyloWS/Resource/Description.pm
• lib/Bio/Phylo/PhyloWS/Service.pm
• lib/Bio/Phylo/PhyloWS/Service/Timetree.pm
• lib/Bio/Phylo/PhyloWS/Service/Tolweb.pm
• lib/Bio/Phylo/PhyloWS/Service/UbioClassificationBank.pm
• lib/Bio/Phylo/PhyloWS/Service/UbioNameBank.pm
• lib/Bio/Phylo/Project.pm
• lib/Bio/Phylo/Set.pm
• lib/Bio/Phylo/Taxa.pm
• lib/Bio/Phylo/Taxa/TaxaLinker.pm
• lib/Bio/Phylo/Taxa/Taxon.pm
• lib/Bio/Phylo/Taxa/TaxonLinker.pm
• lib/Bio/Phylo/Treedrawer.pm
• lib/Bio/Phylo/Treedrawer/Abstract.pm
• lib/Bio/Phylo/Treedrawer/Canvas.pm
• lib/Bio/Phylo/Treedrawer/Gif.pm
• lib/Bio/Phylo/Treedrawer/Jpeg.pm
• lib/Bio/Phylo/Treedrawer/Pdf.pm
• lib/Bio/Phylo/Treedrawer/Png.pm
• lib/Bio/Phylo/Treedrawer/Processing.pm
• lib/Bio/Phylo/Treedrawer/Svg.pm
• lib/Bio/Phylo/Treedrawer/Swf.pm
• lib/Bio/Phylo/Unparsers/Abstract.pm
• lib/Bio/Phylo/Unparsers/Adjacency.pm
• lib/Bio/Phylo/Unparsers/Cdao.pm
• lib/Bio/Phylo/Unparsers/Fasta.pm
• lib/Bio/Phylo/Unparsers/Figtree.pm
• lib/Bio/Phylo/Unparsers/Hennig86.pm
• lib/Bio/Phylo/Unparsers/Html.pm
• lib/Bio/Phylo/Unparsers/Json.pm
• lib/Bio/Phylo/Unparsers/Mrp.pm
• lib/Bio/Phylo/Unparsers/Newick.pm
• lib/Bio/Phylo/Unparsers/Nexml.pm
• lib/Bio/Phylo/Unparsers/Nexus.pm
• lib/Bio/Phylo/Unparsers/Nhx.pm
• lib/Bio/Phylo/Unparsers/Nwmsrdf.pm
• lib/Bio/Phylo/Unparsers/Pagel.pm
• lib/Bio/Phylo/Unparsers/Phylip.pm
• lib/Bio/Phylo/Unparsers/Phyloxml.pm
• lib/Bio/Phylo/Unparsers/Rss1.pm
• lib/Bio/Phylo/Unparsers/Taxlist.pm
• lib/Bio/Phylo/Util/CONSTANT.pm
• lib/Bio/Phylo/Util/CONSTANT/Int.pm
• lib/Bio/Phylo/Util/Dependency.pm
• lib/Bio/Phylo/Util/Exceptions.pm
• lib/Bio/Phylo/Util/IDPool.pm
• lib/Bio/Phylo/Util/Logger.pm
• lib/Bio/Phylo/Util/MOP.pm
• lib/Bio/Phylo/Util/Math.pm
• lib/Bio/Phylo/Util/OptionalInterface.pm
• lib/Bio/Phylo/Util/StackTrace.pm
• lib/Bio/PhyloRole.pm
• t/00-load.t
• t/01-phylo.t
• t/02-newick.t
• t/03-node.t
• t/04-generator.t
• t/05-trees.t
• t/06-tree.t
• t/07-unparse.t
• t/08-datum.t
• t/09-matrix.t
• t/10-matrices.t
• t/11-taxon.t
• t/12-taxa.t
• t/13-listable.t
• t/14-nexus.t
• t/15-table.t
• t/16-unparse.t
• t/17-parse.t
• t/18-taxlist.t
• t/19-svg.t
• t/20-nexml.t
• t/21-bioperl-tree.t
• t/22-bioperl-node.t
• t/23-bioperl-treeio.t
• t/24-bioperl-alignio.t
• t/25-dom-mapping.t
• t/26-dom.t
• t/28-reroot.t
• t/29-treemodels.t
• t/30-phyloxml.t
• t/31-phylip.t
• t/32-tolweb.t
• t/33-models.t
• t/34-json.t
• t/35-processing.t
• t/36-sets.t
• t/37-memory.t
• t/38-rdf.t
• t/39-nexussets.t
• t/40-hennig86.t
• t/41-charstatelabels.t
• t/42-simplify-newick.t
• t/43-adjacency.t
• t/44-tnrs.t
• t/45-fastq.t
• t/46-noformat.t
• t/47-clone.t
• t/48-drawnoderole.t
• t/49-drawtreerole.t
• t/50-replicate-tree.t
• t/51-replicate-binary.t
• t/52-replicate-dna.t
• t/53-more-matrix.t
• t/54-rankprob.t
• t/55-modeltest.t
• t/56-figtree.t
• t/57-nhx.t
• t/58-symdiff.t
• t/59-yandell.t
• t/60-dwca.t
• t/perl-critic.t
• t/perlcriticrc
• t/pod-coverage.t
• t/pod.t
• t/regress_18208.t
• t/regress_21209.t
• t/regress_21417.t
• t/regress_22813.t
• t/regress_35511.t
• t/regress_41070.t
• t/regress_51602.t
• t/regress_52960.t