The Bioperl Project is an international association of users & developers of open source Perl tools for bioinformatics, genomics and life science

This is a HOWTO that talks about using Bioperl, for biologists who would like to learn more about writing their own bioinformatics scripts using Bioperl. Bioperl is an open source bioinformatics toolkit used by researchers all over the world.

Beginners HOWTO - Introduction to BioPerl for biologists. Features and Annotations HOWTO - Reading and writing detailed data associated with sequences. BlastPlus HOWTO - Create, manage, and query BLAST databases with NCBI blast+.

BIOPERL INSTALLATION. The following are instructions for installing BioPerl on Unix, Linux, and Mac OS X. README.md

The SeqIO system handles sequences of many different formats and is the way Bioperl pushes sequences in and out of objects. You can think of the SeqIO system as “a smart filehandle for sequences”.

An effort is currently under way to gather all the world’s collected wisdom about biological data into a set of modules called “bioPerl” (discussed at length in an article to be published later in the Perl Journal). Perl is easy to write and fast to develop in.

This is a HOWTO that talks about using Bioperl and tools related to Bioperl to get genomic sequence. There are a few different approaches, one uses files that you’ll download to your own computer to query locally, others use remote, programmable interfaces or APIs .

The Bioperl parsers for Genbank and EMBL are built to respect the specification for the feature tables agreed upon by Genbank, EMBL, and DDBJ (see the Feature Table Definition for the details). Check this page if you’re interested in a complete listing and description of all the Genbank, EMBL, and DDBJ feature tags.

This page is a list of ‘‘best practices’’ for anyone contributing to Bioperl. Also see Advanced BioPerl and the Using Git HOWTO. Style. Use spaces instead of tabs for indenting; Prefix protected/private subroutines/fields with an underscore; Interface modules end with a capital “I”, e.g. Bio::LocationI

This HOWTO intends to show how to use the BioPerl Tree objects to manipulate phylogenetic trees. It shows how to read and write trees, query them for information about specific nodes or overall statistics, and create pictures of trees.