Kozo Nishida edited this page Jun 14, 2016 · 2 revisions

BioRuby HOWTOs

HOWTOs translated from BioPerl HOWTOs:

Beginners HOWTO An introduction to BioRuby, 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 BioRuby.

OBDA Access HOWTO Using OBDA, a universal and customizable sequence retrieval system.

Trees HOWTO Using BioRuby to manipulate phylogenetic trees.

PopGen/Perlymorphism HOWTO Population genetics, molecular evolution, and BioRuby.

Graphics HOWTO Creating beautiful graphics for sequence display and annotation.

Custom Glyphs HOWTO Extend [http://www.bioperl.org/wiki/Module:Bio::Graphics Bio::Graphics (BioPerl)] using custom glyphs (advanced).

Build Pipelines for Phylogenetic analyses HOWTO A framework for phylogenetic analyses from gene set to gene family to alignment to phylogenetic inference.

Using EUtilities HOWTO A guide on how to use [http://www.bioperl.org/wiki/Module:Bio::DB::EUtilities Bio::DB::EUtilities (BioPerl)] 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 BioRuby.

Copyright notice

The above HOWTOs are based on BioPerl HOWTOs. Therefore, copyright notice for BioPerl HOWTOs described below is also applied to the above HOWTOs.

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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