Bio-Phylo 0.50
- Released by
- RVOSA
- Version
- Release Date
- 2012-06-12
- Kwalitee
- 134.38
- Core Kwalitee
- 87.5
- LINKS
Bio-Phylo 0.50 Deleted
Kwalitee Issues
- meta_yml_conforms_to_known_spec
-
Take a look at the META.yml Spec at https://metacpan.org/pod/CPAN::Meta::History::Meta_1_4 (for version 1.4) or https://metacpan.org/pod/CPAN::Meta::Spec (for version 2), and change your META.yml accordingly.
Error: Missing mandatory field, 'abstract' (abstract) [Validation: 1.4];value is an undefined string (abstract) [Validation: 1.4]
- has_changelog
-
Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.
- use_strict
-
Add 'use strict' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules are strictly written.
Error: Bio::Phylo::Identifiable, Bio::Phylo::Util::Dependency
- no_pod_errors
-
Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.
Error: Bio-Phylo-0.50/lib/Bio/Phylo.pm -- Around line 384: Expected text after =item, not a bullet Around line 389: Expected text after =item, not a bullet Around line 394: Expected text after =item, not a bullet
- meta_yml_declares_perl_version
-
If you are using Build.PL define the {requires}{perl} = VERSION field. If you are using MakeMaker (Makefile.PL) you should upgrade ExtUtils::MakeMaker to 6.48 and use MIN_PERL_VERSION parameter. Perl::MinimumVersion can help you determine which version of Perl your module needs.
- has_meta_json
-
Add a META.json to the distribution. Your buildtool should be able to autogenerate it.
- use_warnings
-
Add 'use warnings' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.
Error: Bio::Phylo, Bio::Phylo::Factory, Bio::Phylo::Forest, Bio::Phylo::Forest::DrawNode, Bio::Phylo::Forest::DrawTree, Bio::Phylo::Forest::Node, Bio::Phylo::Forest::Tree, Bio::Phylo::Generator, Bio::Phylo::IO, Bio::Phylo::Identifiable, Bio::Phylo::Listable, Bio::Phylo::Matrices, Bio::Phylo::Matrices::Character, Bio::Phylo::Matrices::Characters, Bio::Phylo::Matrices::Datatype, Bio::Phylo::Matrices::Datatype::Continuous, Bio::Phylo::Matrices::Datatype::Custom, Bio::Phylo::Matrices::Datatype::Dna, Bio::Phylo::Matrices::Datatype::Mixed, Bio::Phylo::Matrices::Datatype::Protein, Bio::Phylo::Matrices::Datatype::Restriction, Bio::Phylo::Matrices::Datatype::Rna, Bio::Phylo::Matrices::Datatype::Standard, Bio::Phylo::Matrices::Datum, Bio::Phylo::Matrices::Matrix, Bio::Phylo::Matrices::TypeSafeData, Bio::Phylo::Mediators::TaxaMediator, 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, Bio::Phylo::NeXML::DOM::Document, Bio::Phylo::NeXML::DOM::Document::Libxml, Bio::Phylo::NeXML::DOM::Document::Twig, Bio::Phylo::NeXML::DOM::Element, Bio::Phylo::NeXML::DOM::Element::Libxml, Bio::Phylo::NeXML::DOM::Element::Twig, Bio::Phylo::NeXML::Entities, Bio::Phylo::NeXML::Meta, Bio::Phylo::NeXML::Meta::XMLLiteral, Bio::Phylo::NeXML::Writable, Bio::Phylo::Parsers::Abstract, Bio::Phylo::Parsers::Adjacency, Bio::Phylo::Parsers::Fasta, Bio::Phylo::Parsers::Json, Bio::Phylo::Parsers::Nexml, Bio::Phylo::Parsers::Nexus, Bio::Phylo::Parsers::Phylip, Bio::Phylo::Parsers::Phyloxml, Bio::Phylo::Parsers::Table, Bio::Phylo::Parsers::Taxlist, Bio::Phylo::Parsers::Tnrs, Bio::Phylo::Parsers::Tolweb, Bio::Phylo::Parsers::Ubiocbmeta, Bio::Phylo::Parsers::Ubiometa, Bio::Phylo::Parsers::Ubiosearch, Bio::Phylo::PhyloWS, Bio::Phylo::PhyloWS::Client, Bio::Phylo::PhyloWS::Resource, Bio::Phylo::PhyloWS::Resource::Description, Bio::Phylo::PhyloWS::Service, Bio::Phylo::PhyloWS::Service::Timetree, Bio::Phylo::PhyloWS::Service::Tolweb, Bio::Phylo::PhyloWS::Service::UbioClassificationBank, Bio::Phylo::PhyloWS::Service::UbioNameBank, Bio::Phylo::Project, Bio::Phylo::Set, Bio::Phylo::Taxa, Bio::Phylo::Taxa::TaxaLinker, Bio::Phylo::Taxa::Taxon, Bio::Phylo::Taxa::TaxonLinker, Bio::Phylo::Treedrawer, Bio::Phylo::Treedrawer::Abstract, Bio::Phylo::Treedrawer::Canvas, Bio::Phylo::Treedrawer::Gif, Bio::Phylo::Treedrawer::Jpeg, Bio::Phylo::Treedrawer::Pdf, Bio::Phylo::Treedrawer::Png, Bio::Phylo::Treedrawer::Processing, Bio::Phylo::Treedrawer::Svg, Bio::Phylo::Treedrawer::Swf, Bio::Phylo::Unparsers::Abstract, Bio::Phylo::Unparsers::Adjacency, Bio::Phylo::Unparsers::Cdao, Bio::Phylo::Unparsers::Fasta, Bio::Phylo::Unparsers::Hennig86, Bio::Phylo::Unparsers::Html, Bio::Phylo::Unparsers::Json, Bio::Phylo::Unparsers::Mrp, Bio::Phylo::Unparsers::Newick, Bio::Phylo::Unparsers::Nexml, Bio::Phylo::Unparsers::Nexus, Bio::Phylo::Unparsers::Pagel, Bio::Phylo::Unparsers::Phylip, Bio::Phylo::Unparsers::Phyloxml, Bio::Phylo::Unparsers::Rss1, Bio::Phylo::Unparsers::Taxlist, Bio::Phylo::Util::CONSTANT, Bio::Phylo::Util::Dependency, Bio::Phylo::Util::Exceptions, Bio::Phylo::Util::IDPool, Bio::Phylo::Util::Logger, Bio::Phylo::Util::OptionalInterface, Bio::Phylo::Util::StackTrace
- no_invalid_versions
-
Fix the version numbers so that version::is_lax($version) returns true.
Error:
- lib/Bio/Phylo/EvolutionaryModels.pm: HASH(0x55607d517388)
- 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.
- meta_yml_has_repository_resource
-
Add a 'repository' resource to the META.yml via 'meta_add' accessor (for Module::Build) or META_ADD parameter (for ExtUtils::MakeMaker).
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| Bio::Phylo | Phylogenetic analysis using perl | 0.50 | 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::DrawNode | Tree node with extra methods for tree drawing | metacpan | |
| Bio::Phylo::Forest::DrawTree | Tree with extra methods for tree drawing | metacpan | |
| Bio::Phylo::Forest::Node | Node in a phylogenetic tree | metacpan | |
| Bio::Phylo::Forest::Tree | 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::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::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::Standard | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datum | Character state sequence | metacpan | |
| Bio::Phylo::Matrices::Matrix | 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::Dna | metacpan | ||
| Bio::Phylo::Models::Substitution::Dna::F81 | metacpan | ||
| Bio::Phylo::Models::Substitution::Dna::GTR | metacpan | ||
| Bio::Phylo::Models::Substitution::Dna::HKY85 | metacpan | ||
| Bio::Phylo::Models::Substitution::Dna::JC69 | metacpan | ||
| Bio::Phylo::Models::Substitution::Dna::K80 | 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::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::Fasta | 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::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::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::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::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::OptionalInterface | Utility class for managing optional superclasses. No serviceable parts inside. | metacpan | |
| Bio::Phylo::Util::StackTrace | Stack traces for exceptions | metacpan |