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http://cliiq.sourceforge.net/Home
An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population.
Proper citation: CLIIQ (RRID:SCR_009972) Copy
http://sourceforge.net/p/mira-assembler/wiki/Home/
Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data.
Proper citation: MIRA (RRID:SCR_010731) Copy
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
Standard specification for the information required to report a genotyping experiment, covering: study and experiment design, subject information, genotyping procedure, and data analysis methods. The goal is to set a reporting standard for adoption by the research community to facilitate consistent data interpretation and independent validation/reproduction, and to serve as guidance for database design for storing genotyping experiment data. MIGen is being developed as a collaborative project involving international domain experts and is a registered project under MIBBI: Minimum Information for Biological and Biomedical Investigations.
Proper citation: MIGen (RRID:SCR_006959) Copy
http://samtools.sourceforge.net/
A generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms.
Proper citation: SAM format (RRID:SCR_012093) 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
http://ipapers.sourceforge.net/iPapers.html
Software application that manages many PDF files of articles, whose information can be obtained by PubMed.
Proper citation: iPapers (RRID:SCR_012103) Copy
http://sourceforge.net/projects/phylotreepruner/
A utility that uses a phylogenetic approach to refine orthology inferences made by graph-based (or other) methods.
Proper citation: PhyloTreePruner (RRID:SCR_012069) Copy
http://sourceforge.net/projects/coperead/
An efficient software tool to connect overlapping pair-end reads using k-mer frequencies.
Proper citation: Connecting Overlapped Pair-End reads (RRID:SCR_012102) Copy
http://sourceforge.net/projects/raspnmr/
Software that uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy.
Proper citation: RASP (RRID:SCR_012062) Copy
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