Practical descriptions of BioPerl modules with a focus on common tasks.

• 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+.
• EUtilities Cookbook HOWTO - Simple script examples using Bio::DB::EUtilities.
• SearchIO HOWTO - Parsing reports from sequence comparison programs like BLAST.
• SeqIO HOWTO - Sequence file input and output, with script examples.
• Getting Genomic Sequences HOWTO - Some examples of how to retrieve genomic sequences.
• AlignIO and SimpleAlign HOWTO - Create and analyze alignments using BioPerl.
• Writing BioPerl Tests HOWTO - A general guide on how to write BioPerl tests using Test::More.
• OBDA Flat Databases HOWTO - Indexing local sequence files for fast retrieval using OBDA.
• Tiling HOWTO - Use SearchIO to create robust alignments.
• Local Databases - Indexing local sequence files for fast retrieval.
• OBDA HOWTO - Using OBDA, a universal and customizable sequence retrieval system.
• Restriction Enzyme Analysis HOWTO - in silico restriction enzyme analysis.
• Short-read assemblies with BWA HOWTO - Using the bwa assembler in BioPerl.
• Short-read assemblies with maq HOWTO - Using the maq assembler in BioPerl.
• Trees HOWTO - Using BioPerl to analyze phylogenetic trees.
• EUtilities Web Service HOWTO - Query NCBI Entrez via the EUtilities.
• PAML HOWTO - Using the PAML package using BioPerl.
• PhyloXML HOWTO - Read and write phyloXML documents using BioPerl.
• Bioperl Objects HOWTO - The common and uncommon objects that represent sequence.
• Simple Web Analysis HOWTO - Submitting sequence data to Web forms and retrieving results.
• Best Practices HOWTO - The conventions to use when writing BioPerl code.
• Advanced BioPerl HOWTO - Notes on developing BioPerl code.
• PopGen HOWTO - Population genetics, molecular evolution, and BioPerl.
• SubmitPatch HOWTO - The steps needed to get your modification to BioPerl into the code base.
• Nexml HOWTO - A guide on how to read and write Nexml documents using BioPerl.
• Glyphs HOWTO - Extend Bio::Graphics using custom glyphs.
• BioGraphics HOWTO - Creating beautiful graphics for sequence display and annotation.
• Using Git HOWTO - Using Git with BioPerl.
• Submitting Issues HOWTO - How we suggest submission of bugs and feature requests.
• Scrapbook HOWTO - Donated scraps of BioPerl code for you to reuse.

Instructions for BioPerl developers and maintainers

• Splitting a subset of modules into a new distribution

• Sequence format examples