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http://matnmr.sourceforge.net/
A highly flexible software toolbox for processing 1D and 2D NMR and EPR spectra under MATLAB, creating high-quality 1D, 2D or 3D plots from the spectra and printing them in every type of format that is supported by MATLAB.
Proper citation: MatNMR (RRID:SCR_012060) Copy
http://genotan.sourceforge.net/
A free software tool to identify length variation of microsatellites from short sequence reads.
Proper citation: GenoTan (RRID:SCR_007935) Copy
A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
Proper citation: BRIG (RRID:SCR_007802) Copy
http://seqpig.sourceforge.net/
A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters.
Proper citation: SeqPig (RRID:SCR_008548) Copy
http://sourceforge.net/projects/glprobs/
Software implementing a simple and effective approach to improve the accuracy of multiple sequence alignment.
Proper citation: GLProbs (RRID:SCR_002739) Copy
A fast and versatile Open Source docking software program that can be used to dock small molecules against proteins and nucleic acids.
Proper citation: rDock (RRID:SCR_002838) Copy
http://contra-cnv.sourceforge.net/
A tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.
Proper citation: CONTRA (RRID:SCR_010814) Copy
http://svdetect.sourceforge.net/Site/Home.html
Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads.
Proper citation: SVDetect (RRID:SCR_010812) Copy
http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Page
A de novo whole-genome shotgun (WGS) DNA sequence assembler.
Proper citation: Celera assembler (RRID:SCR_010750) Copy
http://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=FindPeaks
Software application that can be used for converting Eland, Maq (.map), BED or other files into WIG files and identifying areas of enrichment (ChIP-Seq analysis).
Proper citation: FindPeaks (RRID:SCR_010857) Copy
http://genovar.sourceforge.net/
A Detection and Visualization software tool for Genomic Variants.
Proper citation: Genovar (RRID:SCR_010930) Copy
http://ranger.sourceforge.net/
Software for a multi-purpose ChIP Seq peak caller.
Proper citation: PeakRanger (RRID:SCR_010863) Copy
http://biodoop-seal.sourceforge.net/
A suite of distributed software applications for aligning short DNA reads, and manipulating and analyzing short read alignments.
Proper citation: SEAL (RRID:SCR_010914) Copy
http://sourceforge.net/apps/mediawiki/cloudburst-bio/index.php?title=CloudBurst
A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.
Proper citation: CloudBurst (RRID:SCR_010911) Copy
A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads.
Proper citation: ERNE (RRID:SCR_010912) Copy
http://dnptrapper.sourceforge.net/
An assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
Proper citation: DNPTrapper (RRID:SCR_010981) Copy
http://sourceforge.net/apps/mediawiki/amos/index.php?title=Hawkeye
A visual analytics tool for genome assembly analysis and validation, designed to aid in identifying and correcting assembly errors.
Proper citation: Hawkeye (RRID:SCR_010982) Copy
http://mzmine.sourceforge.net/
Software for mass-spectrometry data processing, with the main focus on LC-MS data.
Proper citation: MZmine (RRID:SCR_012040) Copy
http://sourceforge.net/projects/exorca/
A Matlab package extending the scope of established COBRA metabolic modelling.
Proper citation: ORCA (RRID:SCR_012097) Copy
http://opencobra.sourceforge.net/openCOBRA/Welcome.html
Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods.
Proper citation: COBRApy (RRID:SCR_012096) Copy
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