biology/p5-Bio-Phylo 2.0.1 FreeBSD

Phylogenetic analysis using Perl

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
License: ART10, GPLv1+
Categories: biology, perl5
Package size: 542.0 KiB, 1697.0 KiB installed

Description

This is the base class for the Bio::Phylo package. All other modules inherit from it, the methods defined here are applicable to all. Consult the manual for usage examples: Bio::Phylo::Manual.

In the other systems

The newest version among them is 2.0.1, as upstream numbers it.

System

Port

Version

Vulnerabilities

Status

Maintainer

Last update

FreeBSD

biology/p5-Bio-Phylo

2.0.1 newest

none known

[email protected]

DragonFly

biology/p5-Bio-Phylo

2.0.1 newest

none known

[email protected]

HardenedBSD

biology/p5-Bio-Phylo

2.0.1 newest

no data

[email protected]

GhostBSD

biology/p5-Bio-Phylo

2.0.1 newest

no data

[email protected]

Install

Binary package:

pkg install p5-Bio-Phylo

From the ports tree:

cd /usr/ports/biology/p5-Bio-Phylo/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	p5-Bio-Phylo>0:biology/p5-Bio-Phylo

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repository	aarch64	amd64	armv6	armv7	i386
FreeBSD:14:latest	2.0.1	2.0.1	2.0.1	-	2.0.1
FreeBSD:14:quarterly	2.0.1	2.0.1	n/a	-	2.0.1
FreeBSD:15:latest	2.0.1	2.0.1	n/a	-	2.0.1
FreeBSD:15:quarterly	2.0.1	2.0.1	n/a	n/a	n/a
FreeBSD:16:latest	2.0.1	2.0.1	n/a	n/a	n/a
FreeBSD:16:quarterly	n/a	n/a	n/a	n/a	n/a

Dependency graph

Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.

graph LR
  me["biology/p5-Bio-Phylo"]
  me --> d0["archivers/brotli"]
  me --> d1["archivers/libdeflate"]
  me --> d2["archivers/liblz4"]
  me --> d3["archivers/p5-Archive-Zip"]
  me --> d4["archivers/zstd"]
  me --> d5["biology/p5-BioPerl"]
  me --> d6["converters/libiconv"]
  me --> d7["converters/p5-Encode-Locale"]
  me -.-> dmore(["172 more"])
  classDef this fill:#ab2b28,color:#ffffff,stroke:#ab2b28
  class me this

Dependencies

As this port's Makefile names them.

Build 14

p5-Archive-Zip>=0 : archivers/p5-Archive-Zip
p5-BioPerl>=0 : biology/p5-BioPerl
p5-GD>=0 : graphics/p5-GD
p5-Math-CDF>=0 : math/p5-Math-CDF
p5-Math-Random>=0 : math/p5-Math-Random
p5-PDF-API2>=0 : textproc/p5-PDF-API2
p5-RDF-Query>=0 : textproc/p5-RDF-Query
p5-RDF-Trine>=0 : textproc/p5-RDF-Trine
p5-SVG>=0 : textproc/p5-SVG
p5-SWF-Builder>=0 : graphics/p5-SWF-Builder
p5-XML-LibXML>=0 : textproc/p5-XML-LibXML
p5-XML-Twig>=0 : textproc/p5-XML-Twig
p5-XML-XML2JSON>=0 : textproc/p5-XML-XML2JSON
p5-libxml>=0 : textproc/p5-libxml

Runtime 14

p5-Archive-Zip>=0 : archivers/p5-Archive-Zip
p5-BioPerl>=0 : biology/p5-BioPerl
p5-GD>=0 : graphics/p5-GD
p5-Math-CDF>=0 : math/p5-Math-CDF
p5-Math-Random>=0 : math/p5-Math-Random
p5-PDF-API2>=0 : textproc/p5-PDF-API2
p5-RDF-Query>=0 : textproc/p5-RDF-Query
p5-RDF-Trine>=0 : textproc/p5-RDF-Trine
p5-SVG>=0 : textproc/p5-SVG
p5-SWF-Builder>=0 : graphics/p5-SWF-Builder
p5-XML-LibXML>=0 : textproc/p5-XML-LibXML
p5-XML-Twig>=0 : textproc/p5-XML-Twig
p5-XML-XML2JSON>=0 : textproc/p5-XML-XML2JSON
p5-libxml>=0 : textproc/p5-libxml

Test 1

p5-JSON>=0 : converters/p5-JSON

The full lists below include those, and their dependencies in turn.

Build dependencies 180

The first 100 are listed.

Run dependencies 180

The first 100 are listed.

No port depends on this one.

Configuration

No options to configure.

USES: perl5
Service scripts: none

Files

pkg-plist 264

%%SITE_PERL%%/Bio/Phylo.pm
%%SITE_PERL%%/Bio/Phylo/EvolutionaryModels.pm
%%SITE_PERL%%/Bio/Phylo/Factory.pm
%%SITE_PERL%%/Bio/Phylo/Forest.pm
%%SITE_PERL%%/Bio/Phylo/Forest/DrawNodeRole.pm
%%SITE_PERL%%/Bio/Phylo/Forest/DrawTreeRole.pm
%%SITE_PERL%%/Bio/Phylo/Forest/Node.pm
%%SITE_PERL%%/Bio/Phylo/Forest/NodeRole.pm
%%SITE_PERL%%/Bio/Phylo/Forest/Tree.pm
%%SITE_PERL%%/Bio/Phylo/Forest/TreeRole.pm
%%SITE_PERL%%/Bio/Phylo/Generator.pm
%%SITE_PERL%%/Bio/Phylo/IO.pm
%%SITE_PERL%%/Bio/Phylo/Identifiable.pm
%%SITE_PERL%%/Bio/Phylo/Listable.pm
%%SITE_PERL%%/Bio/Phylo/ListableRole.pm
%%SITE_PERL%%/Bio/Phylo/Manual.pod
%%SITE_PERL%%/Bio/Phylo/Matrices.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Character.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Characters.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Continuous.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Custom.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Dna.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Illumina.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Mixed.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Protein.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Restriction.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Rna.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Sanger.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Solexa.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Standard.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datum.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/DatumRole.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Matrix.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/MatrixRole.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/TypeSafeData.pm
%%SITE_PERL%%/Bio/Phylo/Mediators/TaxaMediator.pm
%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Binary.pm
%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna.pm
%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna/F81.pm
%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna/GTR.pm
%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna/HKY85.pm
%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna/JC69.pm
%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna/K80.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/DOM.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document/Libxml.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document/Twig.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element/Libxml.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element/Twig.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/Entities.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/Meta.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/Meta/XMLLiteral.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/Writable.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/XML2JSON.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Abstract.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Adjacency.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Cdao.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Dwca.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Fasta.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Fastq.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Figtree.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Json.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Newick.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Nexml.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Nexus.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Nhx.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Phylip.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Phyloxml.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Table.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Taxlist.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Tnrs.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Tolweb.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Ubiocbmeta.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Ubiometa.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Ubiosearch.pm
%%SITE_PERL%%/Bio/Phylo/PhyloWS.pm
%%SITE_PERL%%/Bio/Phylo/PhyloWS/Client.pm
%%SITE_PERL%%/Bio/Phylo/PhyloWS/Resource.pm
%%SITE_PERL%%/Bio/Phylo/PhyloWS/Resource/Description.pm
%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service.pm
%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/Timetree.pm
%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/Tolweb.pm
%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/UbioClassificationBank.pm
%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/UbioNameBank.pm
%%SITE_PERL%%/Bio/Phylo/Project.pm
%%SITE_PERL%%/Bio/Phylo/Set.pm
%%SITE_PERL%%/Bio/Phylo/Taxa.pm
%%SITE_PERL%%/Bio/Phylo/Taxa/TaxaLinker.pm
%%SITE_PERL%%/Bio/Phylo/Taxa/Taxon.pm
%%SITE_PERL%%/Bio/Phylo/Taxa/TaxonLinker.pm
%%SITE_PERL%%/Bio/Phylo/Treedrawer.pm
%%SITE_PERL%%/Bio/Phylo/Treedrawer/Abstract.pm
%%SITE_PERL%%/Bio/Phylo/Treedrawer/Canvas.pm
%%SITE_PERL%%/Bio/Phylo/Treedrawer/Gif.pm
%%SITE_PERL%%/Bio/Phylo/Treedrawer/Jpeg.pm
%%SITE_PERL%%/Bio/Phylo/Treedrawer/Pdf.pm
%%SITE_PERL%%/Bio/Phylo/Treedrawer/Png.pm
%%SITE_PERL%%/Bio/Phylo/Treedrawer/Processing.pm

The first 100 are listed.

distinfo 1

File

Size

SHA256

Bio-Phylo-v2.0.1.tar.gz

541665

30bf253800a12ac501222ea42d17612f0557af6329daf05465b538569a894f4d

Master sites 1

CPAN

Commit history 0

No commits in the history this site was built from.