Provides nice, programmatic access to fasta and fastq files, as well as providing Sequence and Quality helper classes. No need for BioRuby ;)

Commandline tools for proteomics

Useful class or methods used in qu-* projects.

Light wrapper for RFam data in Ruby.

Rewrite of Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~kenji/subst/) in Ruby programming language

Turns scaffolded contigs and annotations into a genome.

Build a genome scaffold using scaffolder and a set of annotated contigs. This tool updates the locations of the contig annotations using the scaffold template as a base.

Useful Helper methods and classes for testing scaffolder.

Binary to use with scaffolder genome scaffolds

A new ESST generator

'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.

Predict silk-like proteins from its amino acid sequence.

Use the snp-search tool to create, import, manipulate and query your SNP database

Systems Biology Library for Ruby

'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.

A comprehensive wrapper w(RNA)pper for various RNA CLI programs.