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http://sourceforge.net/projects/xdrawchem/
A drawing software application designed for drawing and analyzing chemical structures and reactions.
Proper citation: XDrawChem (RRID:SCR_010941) Copy
A software suite including a scalable hierarchical multitasking parallel infrastructure and the classical sequencing algorithms.
Proper citation: PPSEQ (RRID:SCR_010913) Copy
http://sourceforge.net/p/arpeggio/wiki/Home/
Software for harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures.
Proper citation: Arpeggio (RRID:SCR_010876) Copy
http://ebardenovo.sourceforge.net/
Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.
Proper citation: EBARDenovo (RRID:SCR_011890) Copy
http://sourceforge.net/apps/mediawiki/seqgene/?title=SeqGene
An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc.
Proper citation: SeqGene (RRID:SCR_011861) Copy
http://bayescall.sourceforge.net/
An efficient model-based base-calling algorithm for high-throughput sequencing.
Proper citation: naiveBayesCall (RRID:SCR_011866) Copy
http://scalpel.sourceforge.net/
A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina).
Proper citation: Scalpel (RRID:SCR_012107) Copy
http://sourceforge.net/projects/mtoolbox/
Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data.
Proper citation: MToolBox (RRID:SCR_012112) Copy
http://revister.sourceforge.net/
Software for an automated pipeline using a ''local mapping reference reconstruction method'' to revise mismapped or partially misaligned reads at simple tandem repeat loci.
Proper citation: ReviSTER (RRID:SCR_012113) Copy
http://sourceforge.net/projects/snpratiotest/
Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway.
Proper citation: SNP ratio test (RRID:SCR_012070) Copy
http://toxtree.sourceforge.net/
A full-featured and flexible user-friendly open source software application, which is able to estimate toxic hazard by applying a decision tree approach.
Proper citation: Toxtree (RRID:SCR_012086) Copy
http://sourceforge.net/projects/viewmol/
Software providing a graphical front end for computational chemistry programs.
Proper citation: Viewmol (RRID:SCR_012088) Copy
http://toxmatch.sourceforge.net/
A software tool to facilitate chemical similarity calculations.
Proper citation: Toxmatch (RRID:SCR_012087) Copy
http://qutemol.sourceforge.net/
Open source (GPL) software providing an interactive, high quality molecular visualization system.
Proper citation: QuteMol (RRID:SCR_012089) Copy
http://maltcms.sourceforge.net/users/features.html
An application framework mainly suited for developers working in the domain of bioinformatics for metabolomics and proteomics.
Proper citation: Maltcms (RRID:SCR_012057) Copy
http://insilicogenome.sourceforge.net/
A large-scale whole genome simulation tool which generates large numbers of whole genomes with known sequence characteristics based on direct sampling of experimentally known or theorized variations.
Proper citation: FIGG (RRID:SCR_012064) Copy
http://sourceforge.net/projects/diyg/
A modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences.
Proper citation: DIYA (RRID:SCR_012066) Copy
http://fastphylo.sourceforge.net/
A software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a distance matrix.
Proper citation: Fastphylo (RRID:SCR_012068) Copy
http://mrbayes.sourceforge.net/
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.
Proper citation: MrBayes (RRID:SCR_012067) Copy
http://sourceforge.net/projects/mmax2/
A GUI-based text annotation tool for creating and visualizing annotations.
Proper citation: MMAX2 (RRID:SCR_012100) Copy
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