Bio-Phylo 0.14
- Released by
- RVOSA
- Version
- Release Date
- 2006-09-08
- Kwalitee
- 140.62
- Core Kwalitee
- 93.75
- LINKS
Bio-Phylo 0.14 Deleted
Kwalitee Issues
- buildtool_not_executable
-
Change the permissions of Build.PL/Makefile.PL to not-executable.
- 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-0.14/lib/Bio/Phylo/Manual.pod -- Around line 132: Non-ASCII character seen before =encoding in 'façade'. Assuming CP1252
- 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::Forest, Bio::Phylo::Forest::Node, Bio::Phylo::Forest::Tree, Bio::Phylo::Generator, Bio::Phylo::IO, Bio::Phylo::Listable, Bio::Phylo::Matrices, Bio::Phylo::Matrices::Datum, Bio::Phylo::Matrices::Matrix, Bio::Phylo::Parsers::Newick, Bio::Phylo::Parsers::Nexus, Bio::Phylo::Parsers::Table, Bio::Phylo::Parsers::Taxlist, Bio::Phylo::Taxa, Bio::Phylo::Taxa::Taxon, Bio::Phylo::Treedrawer, Bio::Phylo::Treedrawer::Svg, Bio::Phylo::Unparsers::Mrp, Bio::Phylo::Unparsers::Newick, Bio::Phylo::Unparsers::Nexus, Bio::Phylo::Unparsers::Pagel, Bio::Phylo::Util::CONSTANT, Bio::Phylo::Util::Exceptions, Bio::Phylo::Util::IDPool
- consistent_version
-
Split the distribution, or fix the version numbers to make them consistent (use the highest version number to avoid version downgrade).
Error: 0.13_2188,0.14
- has_separate_license_file
-
This is not a critical issue. Currently mainly informative for the CPANTS authors. It might be removed later.
- has_security_doc
-
Add SECURITY(.pod|md). See Software::Security::Policy.
- security_doc_contains_contact
-
Add SECURITY(.pod|md) and add a contact address. See Software::Security::Policy.
- has_contributing_doc
-
Add CONTRIBUTING(.pod|md). See https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors.
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| Bio::Phylo | Phylogenetic analysis using perl. | 0.14 | metacpan |
| Bio::Phylo::Deprecated | metacpan | ||
| Bio::Phylo::Forest | The forest object, a set of phylogenetic trees. | 0.13_2188 | metacpan |
| Bio::Phylo::Forest::Node | The tree node object. | 0.13_2188 | metacpan |
| Bio::Phylo::Forest::Tree | The tree object. | 0.13_2188 | metacpan |
| Bio::Phylo::Generator | Generates random trees. | 0.13_2188 | metacpan |
| Bio::Phylo::IO | Input and output of phylogenetic data. | 0.13_2188 | metacpan |
| Bio::Phylo::Listable | Parent class for listable/iterator objects. | 0.13_2188 | metacpan |
| Bio::Phylo::Matrices | Holds a set of matrix objects. | 0.13_2188 | metacpan |
| Bio::Phylo::Matrices::Alignment | metacpan | ||
| Bio::Phylo::Matrices::CharSeq | metacpan | ||
| Bio::Phylo::Matrices::Datum | The single observations object. | 0.13_2188 | metacpan |
| Bio::Phylo::Matrices::Matrix | Character state matrix, implements Bio::CDAT::CharMatrixI | 0.13_2188 | metacpan |
| Bio::Phylo::Matrices::Matrix::categorical | metacpan | ||
| Bio::Phylo::Matrices::Matrix::continuous | metacpan | ||
| Bio::Phylo::Matrices::Matrix::dna | metacpan | ||
| Bio::Phylo::Matrices::Matrix::protein | metacpan | ||
| Bio::Phylo::Matrices::Matrix::restriction | metacpan | ||
| Bio::Phylo::Matrices::Matrix::rna | metacpan | ||
| Bio::Phylo::Matrices::Matrix::standard | metacpan | ||
| Bio::Phylo::Matrices::Sequence | metacpan | ||
| Bio::Phylo::Parsers | metacpan | ||
| Bio::Phylo::Parsers::Fastnewick | metacpan | ||
| Bio::Phylo::Parsers::Fastnexus | metacpan | ||
| Bio::Phylo::Parsers::Newick | Parses newick trees. No serviceable parts inside. | 0.13_2188 | metacpan |
| Bio::Phylo::Parsers::Nexus | Parses nexus files. No serviceable parts inside. | 0.13_2188 | metacpan |
| Bio::Phylo::Parsers::Table | Parses tab- (or otherwise) delimited matrices. No serviceable parts inside. | 0.13_2188 | metacpan |
| Bio::Phylo::Parsers::Taxlist | Parses lists of taxon names. No serviceable parts inside. | 0.13_2188 | metacpan |
| Bio::Phylo::Taxa | An object-oriented module for managing taxa. | 0.13_2188 | metacpan |
| Bio::Phylo::Taxa::Taxon | The operational taxonomic unit. | 0.13_2188 | metacpan |
| Bio::Phylo::Treedrawer | An object-oriented facade for drawing trees. | 0.13_2188 | metacpan |
| Bio::Phylo::Treedrawer::Svg | Creates svg tree drawings. No serviceable parts inside. | 0.13_2188 | metacpan |
| Bio::Phylo::Unparsers | metacpan | ||
| Bio::Phylo::Unparsers::Mrp | Unparses a forest object into an MRP matrix. No serviceable parts inside. | 0.13_2188 | metacpan |
| Bio::Phylo::Unparsers::Newick | Unparses newick trees. No serviceable parts inside. | 0.13_2188 | metacpan |
| Bio::Phylo::Unparsers::Nexus | Unparses nexus matrices. No serviceable parts inside. | 0.13_2188 | metacpan |
| Bio::Phylo::Unparsers::Pagel | Unparses pagel data files. No serviceable parts inside. | 0.13_2188 | metacpan |
| Bio::Phylo::Util::CONSTANT | This package defines global constants and utility functions that operate on them. | 0.13_2188 | metacpan |
| Bio::Phylo::Util::Exceptions | Exception classes for Bio::Phylo. No serviceable parts inside. | 0.13_2188 | metacpan |
| Bio::Phylo::Util::IDPool | Utility class for generating object IDs | metacpan |