https://github.com/bioperl/bioperl-live

Core BioPerl 1.x code
https://github.com/bioperl/bioperl-live

bioinformatics bioperl perl toolkit

Last synced: 6 months ago
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Core BioPerl 1.x code

• Host: GitHub
• URL: https://github.com/bioperl/bioperl-live
• Owner: bioperl
• Created: 2010-05-12T17:13:10.000Z (over 15 years ago)
• Default Branch: master
• Last Pushed: 2025-04-03T14:41:43.000Z (6 months ago)
• Last Synced: 2025-04-04T00:10:01.639Z (6 months ago)
• Topics: bioinformatics, bioperl, perl, toolkit
• Language: Perl
• Homepage: http://bioperl.org
• Size: 130 MB
• Stars: 306
• Watchers: 52
• Forks: 184
• Open Issues: 54
• Metadata Files:
  • Readme: README.md
  • Changelog: Changes
  • Code of conduct: CODE_OF_CONDUCT.md
  • Authors: AUTHORS

Awesome Lists containing this project

• Awesome-Bioinformatics - Bioperl - International association of users & developers of open source Perl tools for bioinformatics, genomics and life sciences. [ [paper-2002](https://doi.org/10.1101%2Fgr.361602) | [web](https://bioperl.org) ] (Package suites)

README

          
[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.16344.svg)](http://dx.doi.org/10.5281/zenodo.16344)

[![Build Status](https://github.com/bioperl/bioperl-live/actions/workflows/ci.yml/badge.svg)](https://github.com/bioperl/bioperl-live/actions/workflows/ci.yml)

[![Coverage Status](https://coveralls.io/repos/bioperl/bioperl-live/badge.svg?branch=master)](https://coveralls.io/r/bioperl/bioperl-live?branch=master)

[![Documentation Status](https://readthedocs.org/projects/bioperl/badge/?version=latest)](https://readthedocs.org/projects/bioperl/?badge=latest)

# About BioPerl

BioPerl is a project for development of free and open source Perl

tools for computational molecular biology.  For example, it includes

classes for biological sequences, readers of multiple formats,

sequence alignments, database searching objects, and interfaces to

multiple programs such as EMBOSS, ClustalW, and BLAST.

The BioPerl project has developed multiple module distributions for

different purposes.  The one named BioPerl (named after the project)

provides the foundation for all others distributions.

This is the repository for the BioPerl distribution only.  Other

distributions have [their own

repositories](https://github.com/bioperl/).

# Installation

The BioPerl distribution and BioPerl project have the same name.  The

BioPerl distribution includes only a subset of the project modules.

Because of this, the meaning of "installing BioPerl" is rarely clear.

Instead of "install BioPerl", the aim must be "install module X".

[CPAN.org](https://www.cpan.org/modules/INSTALL.html) provides an

overview on how to install and manage Perl modules but the bottom-line

is:

1. figure out the modules you need, for example `Bio::DB::EUtilities`

   (this is typically the modules that are `use` in your code)

2. install them with `cpanm`, for example `cpanm Bio::DB::EUtilities`

Alternatively, some Linux distributions have packaged BioPerl and have

it available through their package manager.

# Documentation and Support

Documentation for individual modules is in POD and can also be read

online at [metacpan](https://metacpan.org/pod/BioPerl).  Useful

documentation in the form of example code can also be found in the

`examples/` and `bin/` directories.

Additional resources and information about the project is available on

the [project website](https://bioperl.org), with discussion happening

on the [bioperl-l@bioperl.org](mailto:bioperl-l@bioperl.org) mailing

list, and on the `#bioperl` channel of the freenode IRC server.

Bug reports are handle on the distribution github page.

# Development

See the [`HACKING.md`](HACKING.md) file for details on the project

structure, such as building from source and running the test suite.