OBITools is a set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.
Sleipnir is a C++ library enabling efficient analysis, integration, mining, and machine learning over genomic data. This includes a particular focus on microarrays, since they make up the bulk of available data for many organisms, but Sleipnir can also integrate a wide variety of other data types, from pairwise physical interactions to sequence similarity or shared transcription factor binding sites.
COALESCE (Combinatorial Algorithm for Expression and Sequence-based Cluster Extraction) can use large collections of genomic data and Bayesian integration to predict coregulated gene modules, the conditions of regulation, and the consensus binding motifs for regulation.
Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser.
Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is fully Object Oriented and is designed to be both easy to use and computer efficient.
BIU (Bioinformatic Utility Library) is a C++ programming library provides a classes and functions often used in the bioinformatics context. It collects data structures and class hierarchies for biomolecule modelling and general usefull functionalities as program parameter parsing, string conversions, etc.
Wellington is a novel method for the accurate identification of digital genomic footprints from DNase-seq data. pyDNase is an open-source software package which implements the Wellington algorithm to interface with DNase-seq data and expedite analyses.
The rlsim package is a collection of tools for simulating RNA-seq library construction, aiming to reproduce the most important factors which are known to introduce significant biases in the currently used protocols: hexamer priming, PCR amplification and size selection.
Botond Sipos, Tim Massingham and Nick Goldman (2013):
rlsim – a package for simulating RNA-seq library preparation with parameter estimation.
http://bit.ly/rlsim-doc