HOWTOs
From BioPerl
HOWTOs are narrative-based descriptions of BioPerl modules focusing more on a concept or a task than one specific module.
BioPerl HOWTOs
- Beginners HOWTO
- An introduction to BioPerl, including reading and writing sequence files, running and parsing BLAST, retrieving from databases, and more.
- SeqIO HOWTO
- Sequence file I/O, with many script examples.
- SearchIO HOWTO
- Parsing reports from sequence comparison programs like BLAST and writing custom reports.
- Feature-Annotation HOWTO
- Reading and writing detailed data associated with sequences.
- SimpleWebAnalysis HOWTO
- Submitting sequence data to Web forms and retrieving results.
- Flat Databases HOWTO
- Indexing local sequence files for fast retrieval.
- PAML HOWTO
- Using the PAML package using BioPerl.
- OBDA Access HOWTO
- Using OBDA, a universal and customizable sequence retrieval system.
- Trees HOWTO
- Using BioPerl to manipulate phylogenetic trees.
- PopGen/Perlymorphism HOWTO
- Population genetics, molecular evolution, and BioPerl.
- Graphics HOWTO
- Creating beautiful graphics for sequence display and annotation.
- Custom Glyphs HOWTO
- Extend Bio::Graphics using custom glyphs (advanced).
- Submit Patch HOWTO
- The steps needed to get your modification to BioPerl into the code base.
- Build Pipelines for Phylogenetic analyses HOWTO
- A framework for phylogenetic analyses from gene set to gene family to alignment to phylogenetic inference.
- Writing tests for BioPerl modules HOWTO
- A general guide on how to write BioPerl tests using Test::More.
- Using EUtilities HOWTO
- A guide on how to use Bio::DB::EUtilities for retrieving complex data and building customized data pipelines.
- EUtilities Cookbook
- Simple script examples using Bio::DB::EUtilities.
- Getting Genomic Sequences HOWTO
- Some examples of how to retrieve genomic sequences using Bioperl.
Copyright notice
Please note that unless otherwise stated these documents are copyright to a HOWTO author. Please contact them before reproducing or using these documents for anything other than your own personal use.
