Bio-Phylo-v2.0.2/META.json Bio-Phylo-v2.0.2/META.yml COPYING 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/Identifiable.pm lib/Bio/Phylo/IO.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/Math.pm lib/Bio/Phylo/Util/MOP.pm lib/Bio/Phylo/Util/OptionalInterface.pm lib/Bio/Phylo/Util/StackTrace.pm lib/Bio/PhyloRole.pm LICENSE Makefile.PL MANIFEST This list of files README.md 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 META.yml Module YAML meta-data (added by MakeMaker) META.json Module JSON meta-data (added by MakeMaker)