Bio-Phylo v2.0.1
- Released by
- RVOSA
- Version
- Release Date
- 2017-10-31
- Kwalitee
- 156.25
- Core Kwalitee
- 96.88
- LINKS
Bio-Phylo v2.0.1 Latest
Kwalitee Issues
- has_changelog
-
Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.
- meta_yml_has_provides
-
Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| Bio::Phylo | Phylogenetic analysis using perl | 2.000001 | metacpan |
| Bio::Phylo::EvolutionaryModels | Evolutionary models for phylogenetic trees and methods to sample these Klaas Hartmann, September 2007 | metacpan | |
| Bio::Phylo::Factory | Creator of objects, reduces hardcoded class names in code | metacpan | |
| Bio::Phylo::Forest | Container for tree objects | metacpan | |
| Bio::Phylo::Forest::DrawNodeRole | Tree node with extra methods for tree drawing | metacpan | |
| Bio::Phylo::Forest::DrawTreeRole | Tree with extra methods for tree drawing | metacpan | |
| Bio::Phylo::Forest::Node | Node in a phylogenetic tree | metacpan | |
| Bio::Phylo::Forest::NodeRole | Extra behaviours for a node in a phylogenetic tree | metacpan | |
| Bio::Phylo::Forest::Tree | Phylogenetic tree | metacpan | |
| Bio::Phylo::Forest::TreeRole | Extra behaviours for a phylogenetic tree | metacpan | |
| Bio::Phylo::Generator | Generator of tree topologies | metacpan | |
| Bio::Phylo::IO | Front end for parsers and serializers | metacpan | |
| Bio::Phylo::Identifiable | Objects with unique identifiers | metacpan | |
| Bio::Phylo::Listable | List of things, super class for many objects | metacpan | |
| Bio::Phylo::ListableRole | Extra functionality for things that are lists | metacpan | |
| Bio::Phylo::Matrices | Container of matrix objects | metacpan | |
| Bio::Phylo::Matrices::Character | A character (column) in a matrix | metacpan | |
| Bio::Phylo::Matrices::Characters | Container of character objects | metacpan | |
| Bio::Phylo::Matrices::Datatype | Validator of character state data | metacpan | |
| Bio::Phylo::Matrices::Datatype::Continuous | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Custom | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Dna | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Illumina | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Mixed | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Protein | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Restriction | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Rna | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Sanger | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Solexa | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Standard | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datum | Character state sequence | metacpan | |
| Bio::Phylo::Matrices::DatumRole | Extra behaviours for a character state sequence | metacpan | |
| Bio::Phylo::Matrices::Matrix | Character state matrix | metacpan | |
| Bio::Phylo::Matrices::MatrixRole | Extra behaviours for a character state matrix | metacpan | |
| Bio::Phylo::Matrices::TypeSafeData | Superclass for objects that contain character data | metacpan | |
| Bio::Phylo::Mediators::TaxaMediator | Mediator for links between taxa and other objects | metacpan | |
| Bio::Phylo::Models::Substitution::Binary | Binary character substitution model | metacpan | |
| Bio::Phylo::Models::Substitution::Dna | DNA substitution model | metacpan | |
| Bio::Phylo::Models::Substitution::Dna::F81 | Felsenstein (1981) model | metacpan | |
| Bio::Phylo::Models::Substitution::Dna::GTR | General Time Reversible model | metacpan | |
| Bio::Phylo::Models::Substitution::Dna::HKY85 | Hasegawa, Kishino, Yano (1985) model | metacpan | |
| Bio::Phylo::Models::Substitution::Dna::JC69 | Jukes, Cantor (1969) | metacpan | |
| Bio::Phylo::Models::Substitution::Dna::K80 | Kimura 2-parameter | metacpan | |
| Bio::Phylo::NeXML::DOM | XML DOM support for Bio::Phylo | metacpan | |
| Bio::Phylo::NeXML::DOM::Document | XML DOM Abstract class for flexible document object model implementation | metacpan | |
| Bio::Phylo::NeXML::DOM::Document::Libxml | XML DOM document mappings to the C<XML::LibXML> package | metacpan | |
| Bio::Phylo::NeXML::DOM::Document::Twig | XML DOM document mappings to the C<XML::Twig> package | metacpan | |
| Bio::Phylo::NeXML::DOM::Element | XML DOM Abstract class for flexible document object model implementation | metacpan | |
| Bio::Phylo::NeXML::DOM::Element::Libxml | XML DOM element mappings to the C<XML::LibXML> package | metacpan | |
| Bio::Phylo::NeXML::DOM::Element::Twig | XML DOM mappings to the XML::Twig package | metacpan | |
| Bio::Phylo::NeXML::Entities | Functions for dealing with XML entities | metacpan | |
| Bio::Phylo::NeXML::Meta | Single predicate/object annotation, attached to an xml-writable subject | metacpan | |
| Bio::Phylo::NeXML::Meta::XMLLiteral | Annotation value adaptor, no direct usage | metacpan | |
| Bio::Phylo::NeXML::Writable | Superclass for objects that serialize to NeXML | metacpan | |
| Bio::Phylo::NeXML::XML2JSON | Helps convert NeXML to JSON, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Abstract | Superclass for parsers used by Bio::Phylo::IO | metacpan | |
| Bio::Phylo::Parsers::Adjacency | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Cdao | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Dwca | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Fasta | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Fastq | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Figtree | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Json | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Newick | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Nexml | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Nexus | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Nhx | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Phylip | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Phyloxml | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Table | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Taxlist | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Tnrs | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Tolweb | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Ubiocbmeta | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Ubiometa | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Ubiosearch | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::PhyloWS | Base class for phylogenetic web services | metacpan | |
| Bio::Phylo::PhyloWS::Client | Base class for phylogenetic web service clients | metacpan | |
| Bio::Phylo::PhyloWS::Resource | Represents a PhyloWS web resource | metacpan | |
| Bio::Phylo::PhyloWS::Resource::Description | Represents a PhyloWS resource description | metacpan | |
| Bio::Phylo::PhyloWS::Service | Base class for phylogenetic web services | metacpan | |
| Bio::Phylo::PhyloWS::Service::Timetree | PhyloWS service wrapper for Timetree | metacpan | |
| Bio::Phylo::PhyloWS::Service::Tolweb | PhyloWS service wrapper for Tree of Life | metacpan | |
| Bio::Phylo::PhyloWS::Service::UbioClassificationBank | PhyloWS service wrapper for uBio ClassificationBank records | metacpan | |
| Bio::Phylo::PhyloWS::Service::UbioNameBank | PhyloWS service wrapper for uBio NameBank records | metacpan | |
| Bio::Phylo::Project | Container for related data | metacpan | |
| Bio::Phylo::Set | Subset of the parts inside a container | metacpan | |
| Bio::Phylo::Taxa | Container of taxon objects | metacpan | |
| Bio::Phylo::Taxa::TaxaLinker | Superclass for objects that link to taxa objects | metacpan | |
| Bio::Phylo::Taxa::Taxon | Operational taxonomic unit | metacpan | |
| Bio::Phylo::Taxa::TaxonLinker | Superclass for objects that link to taxon objects | metacpan | |
| Bio::Phylo::Treedrawer | Visualizer of tree shapes | metacpan | |
| Bio::Phylo::Treedrawer::Abstract | Abstract graphics writer used by treedrawer, no serviceable parts inside | metacpan | |
| Bio::Phylo::Treedrawer::Canvas | Graphics format writer used by treedrawer, no serviceable parts inside | metacpan | |
| Bio::Phylo::Treedrawer::Gif | Graphics format writer used by treedrawer, no serviceable parts inside | metacpan | |
| Bio::Phylo::Treedrawer::Jpeg | Graphics format writer used by treedrawer, no serviceable parts inside | metacpan | |
| Bio::Phylo::Treedrawer::Pdf | Graphics format writer used by treedrawer, no serviceable parts inside | metacpan | |
| Bio::Phylo::Treedrawer::Png | Graphics format writer used by treedrawer, no serviceable parts inside | metacpan | |
| Bio::Phylo::Treedrawer::Processing | Graphics format writer used by treedrawer, no serviceable parts inside | metacpan | |
| Bio::Phylo::Treedrawer::Svg | Graphics format writer used by treedrawer, no serviceable parts inside | metacpan | |
| Bio::Phylo::Treedrawer::Swf | Graphics format writer used by treedrawer, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Abstract | Superclass for unparsers used by Bio::Phylo::IO | metacpan | |
| Bio::Phylo::Unparsers::Adjacency | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Cdao | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Fasta | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Figtree | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Hennig86 | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Html | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Json | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Mrp | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Newick | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Nexml | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Nexus | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Nhx | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Nwmsrdf | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Pagel | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Phylip | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Phyloxml | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Rss1 | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Taxlist | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Util::CONSTANT | Global constants and utility functions | metacpan | |
| Bio::Phylo::Util::CONSTANT::Int | Integer constants, no serviceable parts inside | metacpan | |
| Bio::Phylo::Util::Dependency | Utility class for importing external dependencies. No serviceable parts inside. | metacpan | |
| Bio::Phylo::Util::Exceptions | Errors ($@) that are objects | metacpan | |
| Bio::Phylo::Util::IDPool | Utility class for generating object IDs. No serviceable parts inside. | metacpan | |
| Bio::Phylo::Util::Logger | Logger of internal messages of several severity levels | metacpan | |
| Bio::Phylo::Util::MOP | Meta-object programming, no serviceable parts inside | metacpan | |
| Bio::Phylo::Util::Math | Utility math functions | metacpan | |
| Bio::Phylo::Util::OptionalInterface | Utility class for managing optional superclasses. No serviceable parts inside. | metacpan | |
| Bio::Phylo::Util::StackTrace | Stack traces for exceptions | metacpan | |
| Bio::PhyloRole | Extra behaviours for the base class | metacpan |