Getting BioPerl
Contents |
BioPerl Packages
- Core package provides the main parsers, this is the basic package and it's required by all the other packages (bioperl-live in Git)
- Run package provides wrappers for executing some 60 common bioinformatics applications (bioperl-run in Git)
- BioPerl db is a subproject to store sequence and annotation data in a BioSQL relational database (bioperl-db in Git).
- Network package parses and analyzes protein-protein interaction data (bioperl-network in Git).
- The Bio::Graphics modules, as of BioPerl-1.6.0, are released independently of bioperl core. You can now obtain them on CPAN.
- Ext package is for C-language extensions including some alignment algorithms and an interface to the Staden IO library (bioperl-ext in Subversion).
- Pedigree package is for manipulating genotype, marker, and individual data for linkage studies (bioperl-pedigree in Subversion)
BioPerl Releases
All current and past distributions are available from the BioPerl Distribution. For more information about the different versions and the stable versus developer distinction please see a related question in the FAQ.
Which version should I get?
- If you are just starting with Bioperl, you should download the stable release as it is the most currently maintained release.
- If you have older scripts and are concerned about API compatibility, you may want install the stable Bioperl.
- Pre-compiled binary packages are available for some systems including Windows, Linux (currently Fedora) and MacOS X.
Bioperl 1.6.1, Stable Release
This represents the latest code from the main development base, released Sep-2009. Only core modules have been released for 1.6 at this time, but the accompanying packages (run,network,db) will be released soon after.
| Core modules | tar.gz | zip | bz2 |
Bioperl 1.5.2, Developer Release
This represents the a code release from the main development base, released Dec-2006.
| Core modules | tar.gz | zip | bz2 |
| Run modules | tar.gz | zip | bz2 |
| DB modules | tar.gz | zip | bz2 |
| Network modules | tar.gz | zip | bz2 |
| C extension modules | tar.gz | zip | bz2 (from Bioperl 1.5.1) |
Other ways to get the releases
All Releases
http://bioperl.org/DIST Checksums
Mirrors
iubio.bio.indiana.edu - Daily updates.
Perl CPAN
Information on how to use CPAN.pm to automatically download BioPerl and various CPAN module dependencies is described in Installing BioPerl.
Version Control System
BioPerl's open source code is managed by the Git version control system, hosted for free by GitHub. This is the source for the very latest, in-development, possibly non-working BioPerl source code. For more about how BioPerl uses git, see Using Git.
Snapshots
These are downloadable copies of the latest in-development, bleeding edge source code. In other words, exactly the same as what you would get via Git above, except conveniently packaged as tarballs or zipballs.
| Core modules | tar.gz | zip |
| Run modules | tar.gz | zip |
| DB modules | tar.gz | zip |
| Network modules | tar.gz | zip |
| C extension modules | tar.gz | zip |
Installation
See: Installing BioPerl
Unsupported Packages
These are older packages that are no longer maintained.
