HOWTOs

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HOWTOs are narrative-based descriptions of BioPerl modules focusing more on a concept or a task than one specific module.

Contents


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.
Tiling HOWTO
Using search reports parsed by SearchIO to obtain robust overall alignment statistics
BlastPlus HOWTO
Using BioPerl to create, manage, and query BLAST databases with the NCBI blast+ suite.
Feature-Annotation HOWTO
Reading and writing detailed data associated with sequences.
SimpleWebAnalysis HOWTO
Submitting sequence data to Web forms and retrieving results.
Local Databases HOWTO
Indexing local sequence files for fast retrieval.
OBDA Flat Databases HOWTO
Indexing local sequence files for fast retrieval using OBDA.
OBDA Access HOWTO
Using OBDA, a universal and customizable sequence retrieval system.
PAML HOWTO
Using the PAML package using BioPerl.
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.
EUtilities Cookbook
Simple script examples using Bio::DB::EUtilities.
Getting Genomic Sequences HOWTO
Some examples of how to retrieve genomic sequences using Bioperl.
EUtilities Web Service HOWTO
Using BioPerl to make and manage NCBI Entrez web service queries via the EUtilities SOAP service.
Short-read assemblies with bwa
How to use the bwa Burrows-Wheeler assembler in BioPerl
Short-read assemblies with maq
How to use the maq assembler in BioPerl
Nexml HOWTO
A guide on how to read/write Nexml documents using BioPerl.
PhyloXML HOWTO
A guide on how to read/write phyloXML documents using BioPerl.
Restriction Enzyme Analysis HOWTO
A guide on how to do in silico restriction enzyme analysis using BioPerl.
Bioperl Objects HOWTO
A guide on the common and uncommon objects that represent sequence.
AlignIO and SimpleAlign HOWTO
A guide on how to create and analyze alignments using BioPerl.

Requested HOWTOs

The following are HOWTOs that have been either requested by the community at large or by the developers (who might find them useful). Feel free to start one up!

Bio::Assembly
Bio::Location, Bio::Coordinate, Bio::Map
Bio::Tools::Run::Primer3

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.

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