Rutger Vos > Bio-Phylo

Bio-Phylo

This Release Bio-Phylo-0.58  [Download] [Browse 27 Mar 2014
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Repository git://github.com/rvosa/bio-phylo.git
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License The Perl 5 License (Artistic 1 & GPL 1)
Special Files
COPYING
LICENSE
Makefile.PL
MANIFEST
META.json

Modules

Bio::Phylo Phylogenetic analysis using perl     0.58
Bio::Phylo::EvolutionaryModels Evolutionary models for phylogenetic trees and methods to sample these Klaas Hartmann, September 2007      
Bio::Phylo::Factory Creator of objects, reduces hardcoded class names in code      
Bio::Phylo::Forest Container for tree objects      
Bio::Phylo::Forest::DrawNodeRole      
Bio::Phylo::Forest::DrawTreeRole      
Bio::Phylo::Forest::Node Node in a phylogenetic tree      
Bio::Phylo::Forest::NodeRole Extra behaviours for a node in a phylogenetic tree      
Bio::Phylo::Forest::Tree Phylogenetic tree      
Bio::Phylo::Forest::TreeRole Extra behaviours for a phylogenetic tree      
Bio::Phylo::Generator Generator of tree topologies      
Bio::Phylo::IO Front end for parsers and serializers      
Bio::Phylo::Identifiable Objects with unique identifiers      
Bio::Phylo::Listable List of things, super class for many objects      
Bio::Phylo::ListableRole Extra functionality for things that are lists      
Bio::Phylo::Matrices Container of matrix objects      
Bio::Phylo::Matrices::Character A character (column) in a matrix      
Bio::Phylo::Matrices::Characters Container of character objects      
Bio::Phylo::Matrices::Datatype Validator of character state data      
Bio::Phylo::Matrices::Datatype::Continuous Validator subclass, no serviceable parts inside      
Bio::Phylo::Matrices::Datatype::Custom Validator subclass, no serviceable parts inside      
Bio::Phylo::Matrices::Datatype::Dna Validator subclass, no serviceable parts inside      
Bio::Phylo::Matrices::Datatype::Illumina Validator subclass, no serviceable parts inside      
Bio::Phylo::Matrices::Datatype::Mixed Validator subclass, no serviceable parts inside      
Bio::Phylo::Matrices::Datatype::Protein Validator subclass, no serviceable parts inside      
Bio::Phylo::Matrices::Datatype::Restriction Validator subclass, no serviceable parts inside      
Bio::Phylo::Matrices::Datatype::Rna Validator subclass, no serviceable parts inside      
Bio::Phylo::Matrices::Datatype::Sanger Validator subclass, no serviceable parts inside      
Bio::Phylo::Matrices::Datatype::Solexa Validator subclass, no serviceable parts inside      
Bio::Phylo::Matrices::Datatype::Standard Validator subclass, no serviceable parts inside      
Bio::Phylo::Matrices::Datum Character state sequence      
Bio::Phylo::Matrices::DatumRole Extra behaviours for a character state sequence      
Bio::Phylo::Matrices::Matrix Character state matrix      
Bio::Phylo::Matrices::MatrixRole Extra behaviours for a character state matrix      
Bio::Phylo::Matrices::TypeSafeData Superclass for objects that contain character data      
Bio::Phylo::Mediators::TaxaMediator Mediator for links between taxa and other objects      
Bio::Phylo::Models::Substitution::Dna      
Bio::Phylo::Models::Substitution::Dna::F81      
Bio::Phylo::Models::Substitution::Dna::GTR      
Bio::Phylo::Models::Substitution::Dna::HKY85      
Bio::Phylo::Models::Substitution::Dna::JC69      
Bio::Phylo::Models::Substitution::Dna::K80      
Bio::Phylo::NeXML::DOM XML DOM support for Bio::Phylo      
Bio::Phylo::NeXML::DOM::Document XML DOM Abstract class for flexible document object model implementation      
Bio::Phylo::NeXML::DOM::Document::Libxml XML DOM document mappings to the XML::LibXML package      
Bio::Phylo::NeXML::DOM::Document::Twig XML DOM document mappings to the XML::Twig package      
Bio::Phylo::NeXML::DOM::Element XML DOM Abstract class for flexible document object model implementation      
Bio::Phylo::NeXML::DOM::Element::Libxml XML DOM element mappings to the XML::LibXML package      
Bio::Phylo::NeXML::DOM::Element::Twig XML DOM mappings to the XML::Twig package      
Bio::Phylo::NeXML::Entities Functions for dealing with XML entities      
Bio::Phylo::NeXML::Meta Single predicate/object annotation, attached to an xml-writable subject      
Bio::Phylo::NeXML::Meta::XMLLiteral Annotation value adaptor, no direct usage      
Bio::Phylo::NeXML::Writable Superclass for objects that serialize to NeXML      
Bio::Phylo::Parsers::Abstract Superclass for parsers used by Bio::Phylo::IO      
Bio::Phylo::Parsers::Adjacency Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Fasta Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Fastq Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Figtree Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Json Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Newick Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Nexml Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Nexus Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Phylip Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Phyloxml Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Table Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Taxlist Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Tnrs Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Tolweb Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Ubiocbmeta Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Ubiometa Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Parsers::Ubiosearch Parser used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::PhyloWS Base class for phylogenetic web services      
Bio::Phylo::PhyloWS::Client Base class for phylogenetic web service clients      
Bio::Phylo::PhyloWS::Resource Represents a PhyloWS web resource      
Bio::Phylo::PhyloWS::Resource::Description Represents a PhyloWS resource description      
Bio::Phylo::PhyloWS::Service Base class for phylogenetic web services      
Bio::Phylo::PhyloWS::Service::Timetree PhyloWS service wrapper for Timetree      
Bio::Phylo::PhyloWS::Service::Tolweb PhyloWS service wrapper for Tree of Life      
Bio::Phylo::PhyloWS::Service::UbioClassificationBank PhyloWS service wrapper for uBio ClassificationBank records      
Bio::Phylo::PhyloWS::Service::UbioNameBank PhyloWS service wrapper for uBio NameBank records      
Bio::Phylo::Project Container for related data      
Bio::Phylo::Set Subset of the parts inside a container      
Bio::Phylo::Taxa Container of taxon objects      
Bio::Phylo::Taxa::TaxaLinker Superclass for objects that link to taxa objects      
Bio::Phylo::Taxa::Taxon Operational taxonomic unit      
Bio::Phylo::Taxa::TaxonLinker Superclass for objects that link to taxon objects      
Bio::Phylo::Treedrawer Visualizer of tree shapes      
Bio::Phylo::Treedrawer::Abstract Abstract graphics writer used by treedrawer, no serviceable parts inside      
Bio::Phylo::Treedrawer::Canvas Graphics format writer used by treedrawer, no serviceable parts inside      
Bio::Phylo::Treedrawer::Gif Graphics format writer used by treedrawer, no serviceable parts inside      
Bio::Phylo::Treedrawer::Jpeg Graphics format writer used by treedrawer, no serviceable parts inside      
Bio::Phylo::Treedrawer::Pdf Graphics format writer used by treedrawer, no serviceable parts inside      
Bio::Phylo::Treedrawer::Png Graphics format writer used by treedrawer, no serviceable parts inside      
Bio::Phylo::Treedrawer::Processing Graphics format writer used by treedrawer, no serviceable parts inside      
Bio::Phylo::Treedrawer::Svg Graphics format writer used by treedrawer, no serviceable parts inside      
Bio::Phylo::Treedrawer::Swf Graphics format writer used by treedrawer, no serviceable parts inside      
Bio::Phylo::Unparsers::Abstract Superclass for unparsers used by Bio::Phylo::IO      
Bio::Phylo::Unparsers::Adjacency Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Unparsers::Cdao Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Unparsers::Fasta Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Unparsers::Hennig86 Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Unparsers::Html Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Unparsers::Json Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Unparsers::Mrp Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Unparsers::Newick Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Unparsers::Nexml Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Unparsers::Nexus Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Unparsers::Nwmsrdf Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Unparsers::Pagel Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Unparsers::Phylip Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Unparsers::Phyloxml Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Unparsers::Rss1 Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Unparsers::Taxlist Serializer used by Bio::Phylo::IO, no serviceable parts inside      
Bio::Phylo::Util::CONSTANT Global constants and utility functions      
Bio::Phylo::Util::CONSTANT::Int Integer constants, no serviceable parts inside      
Bio::Phylo::Util::Dependency Utility class for importing external dependencies. No serviceable parts inside.      
Bio::Phylo::Util::Exceptions Errors ($@) that are objects      
Bio::Phylo::Util::IDPool Utility class for generating object IDs. No serviceable parts inside.      
Bio::Phylo::Util::Logger Logger of internal messages of several severity levels      
Bio::Phylo::Util::MOP Meta-object programming, no serviceable parts inside      
Bio::Phylo::Util::OptionalInterface Utility class for managing optional superclasses. No serviceable parts inside.      
Bio::Phylo::Util::StackTrace Stack traces for exceptions      
Bio::PhyloRole Extra behaviours for the base class      

Documentation

Bio::Phylo::Forest::DrawNode Tree node with extra methods for tree drawing  
Bio::Phylo::Forest::DrawTree Tree with extra methods for tree drawing  
Bio::Phylo::Manual High-level user guide  

Other Files

README.md