biology/p5-Bio-NEXUS 0.78_1 FreeBSD

Object-oriented Perl API for the NEXUS file format

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
Categories: biology, perl5
Package size: 157.0 KiB, 552.7 KiB installed

Description

Bio::NEXUS package provides an object-oriented, Perl-based applications programming interface (API) to the NEXUS file format of Maddison, et al., 1997 (Syst. Biol. 46:590-621). NEXUS is a powerful and extensible format designed for use in evolutionary analysis, including the analysis of molecular sequence data as well as classical morphological and life-history data. NEXUS is the input or output format for software such as PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and so on. This package also contains the demonstration applications nexplot.pl (plot character data with a tree) and nextool.pl (allowing programmatic editing, e.g., selecting particular clades or subsets of data).

In the other systems

The newest version among them is 0.78, as upstream numbers it.

System

Port

Version

Vulnerabilities

Status

Maintainer

Last update

FreeBSD

biology/p5-Bio-NEXUS

0.78_1 newest

none known

[email protected]

DragonFly

biology/p5-Bio-NEXUS

0.78_1 newest

none known

[email protected]

HardenedBSD

biology/p5-Bio-NEXUS

0.78_1 newest

no data

[email protected]

GhostBSD

biology/p5-Bio-NEXUS

0.78_1 newest

no data

[email protected]

Install

Binary package:

pkg install p5-Bio-NEXUS

From the ports tree:

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

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

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

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

0.78_1

FreeBSD:14:quarterly

0.78_1

n/a

0.78_1

FreeBSD:15:latest

0.78_1

n/a

0.78_1

FreeBSD:15:quarterly

0.78_1

n/a

FreeBSD:16:latest

0.78_1

n/a

FreeBSD:16:quarterly

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-NEXUS"]
  me --> d0["devel/p5-Clone-PP"]
  me --> d1["lang/perl5.42"]
  classDef this fill:#ab2b28,color:#ffffff,stroke:#ab2b28
  class me this

Dependencies

As this port's Makefile names them.

Build 1

p5-Clone-PP>=1.02 : devel/p5-Clone-PP

Runtime 1

p5-Clone-PP>=1.02 : devel/p5-Clone-PP

Test 3

p5-Test-Deep>=0.106 : devel/p5-Test-Deep
p5-Test-Pod>=0 : devel/p5-Test-Pod
p5-Test-Pod-Coverage>=0 : devel/p5-Test-Pod-Coverage

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

Build dependencies 2

Run dependencies 2

No port depends on this one.

Configuration

No options to configure.

USES: perl5
Service scripts: none

Files

pkg-plist 62

bin/nex2text_tree.pl
bin/nexplot.pl
bin/nextool.pl
%%SITE_PERL%%/Bio/NEXUS.pm
%%SITE_PERL%%/Bio/NEXUS/AssumptionsBlock.pm
%%SITE_PERL%%/Bio/NEXUS/Block.pm
%%SITE_PERL%%/Bio/NEXUS/CharactersBlock.pm
%%SITE_PERL%%/Bio/NEXUS/CodonsBlock.pm
%%SITE_PERL%%/Bio/NEXUS/DataBlock.pm
%%SITE_PERL%%/Bio/NEXUS/DistancesBlock.pm
%%SITE_PERL%%/Bio/NEXUS/Functions.pm
%%SITE_PERL%%/Bio/NEXUS/HistoryBlock.pm
%%SITE_PERL%%/Bio/NEXUS/Matrix.pm
%%SITE_PERL%%/Bio/NEXUS/NHXCmd.pm
%%SITE_PERL%%/Bio/NEXUS/Node.pm
%%SITE_PERL%%/Bio/NEXUS/NotesBlock.pm
%%SITE_PERL%%/Bio/NEXUS/SetsBlock.pm
%%SITE_PERL%%/Bio/NEXUS/SpanBlock.pm
%%SITE_PERL%%/Bio/NEXUS/TaxUnit.pm
%%SITE_PERL%%/Bio/NEXUS/TaxUnitSet.pm
%%SITE_PERL%%/Bio/NEXUS/TaxaBlock.pm
%%SITE_PERL%%/Bio/NEXUS/Tools/GraphicsParams.pm
%%SITE_PERL%%/Bio/NEXUS/Tools/NexModifier.pm
%%SITE_PERL%%/Bio/NEXUS/Tools/NexPlotter.pm
%%SITE_PERL%%/Bio/NEXUS/Tree.pm
%%SITE_PERL%%/Bio/NEXUS/TreesBlock.pm
%%SITE_PERL%%/Bio/NEXUS/UnalignedBlock.pm
%%SITE_PERL%%/Bio/NEXUS/UnknownBlock.pm
%%SITE_PERL%%/Bio/NEXUS/Util/Exceptions.pm
%%SITE_PERL%%/Bio/NEXUS/Util/Logger.pm
%%SITE_PERL%%/Bio/NEXUS/WeightSet.pm
%%PERL5_MAN3%%/Bio::NEXUS.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::AssumptionsBlock.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::Block.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::CharactersBlock.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::CodonsBlock.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::DataBlock.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::DistancesBlock.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::Functions.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::HistoryBlock.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::Matrix.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::NHXCmd.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::Node.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::NotesBlock.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::SetsBlock.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::SpanBlock.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::TaxUnit.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::TaxUnitSet.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::TaxaBlock.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::Tools::GraphicsParams.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::Tools::NexModifier.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::Tools::NexPlotter.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::Tree.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::TreesBlock.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::UnalignedBlock.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::UnknownBlock.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::Util::Exceptions.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::Util::Logger.3.gz
%%PERL5_MAN3%%/Bio::NEXUS::WeightSet.3.gz
%%PERL5_MAN1%%/nex2text_tree.pl.1.gz
%%PERL5_MAN1%%/nexplot.pl.1.gz
%%PERL5_MAN1%%/nextool.pl.1.gz

distinfo 1

File

Size

SHA256

Bio-NEXUS-0.78.tar.gz

1.033563e+06

a99cda4e97fd40ee0bee05089a034e84280be9532b0300cd98ed16c303bc85dc

Master sites 1

CPAN

Commit history 0

No commits in the history this site was built from.