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http://sourceforge.net/projects/molbiolib/

A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++.

Proper citation: MolBioLib (RRID:SCR_005372) Copy   

•   Source: SciCrunch Registry

http://splitread.sourceforge.net/

Software for detecting INDELs (small insertions and deletion with size less than 50bp) as well as large deletions that are within the coding regions from the exome sequencing data. It also can be applied to the whole genome sequencing data.

Proper citation: SPLITREAD (RRID:SCR_005264) Copy   

•   Source: SciCrunch Registry

http://www.pazar.info/

Database that unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ''boutiques'' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PAZAR (RRID:SCR_005410) Copy   

•   Source: SciCrunch Registry

http://maq.sourceforge.net/

A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.

Proper citation: Maq (RRID:SCR_005485) Copy   

•   Source: SciCrunch Registry

http://chipexo.sourceforge.net/

A bioinformatics tool dedicated to analyze ChIP-exo data: 1) Sequencing depth normalization and nucleotide composition bias correction. 2) Signal consolidation and noise reduction. 3) Single base resolution border detection. 4) Border matching.

Proper citation: MACE (RRID:SCR_005520) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/treq/home/Home/

A software read mapper for high-throughput DNA sequencing reads, in particular one to several hundred nucleotides in length, and for large edit distance between sequencing read and match in the reference genome. It can cope particularly well with indels for single-best hit recall of 200nt reads simulated from the human reference genome. TreQ performs best at a running time comparable to BWA at large edit distance settings.

Proper citation: TreQ (RRID:SCR_005505) Copy   

•   Source: SciCrunch Registry

http://denovoassembler.sourceforge.net/

Software for a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers.

Proper citation: Ray Meta (RRID:SCR_011918) Copy   

•   Source: SciCrunch Registry

http://uc-echo.sourceforge.net/

Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II.

Proper citation: ECHO (RRID:SCR_011851) Copy   

•   Source: SciCrunch Registry

http://tagcleaner.sourceforge.net/

A software tool which can automatically detect and efficiently remove tag sequences from genomic and metagenomic datasets.

Proper citation: TagCleaner (RRID:SCR_011846) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mirplant/

A user-friendly plant miRNA prediction tool.

Proper citation: miRPlant (RRID:SCR_012105) Copy   

•   Source: SciCrunch Registry

http://pypedal.sourceforge.net/

A pedigree analysis software package that provides tools for error checking, mathematical analysis, report generation, pedigree simulation, and data visualization.

Proper citation: PyPedal (RRID:SCR_012104) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/simulatepcr/

Software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as nt.

Proper citation: Simulate PCR (RRID:SCR_012106) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/sat-assembler/

A targeted gene assembly software program which aims to recover gene families of particular interest to biologists.

Proper citation: SAT-Assembler (RRID:SCR_012108) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/fingerid/

A metabolite identification software using tandem mass spectrometry and kernel methods.

Proper citation: FingerID (RRID:SCR_012077) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/protrac/

A software which detects and analyses piRNA clusters based on quantifiable deviations from a hypothetical uniform distribution regarding the decisive piRNA cluster characteristics.

Proper citation: proTRAC (RRID:SCR_012078) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/netmode/

Fast motif detection algorithm for subgraph size no more than 6.

Proper citation: NetMODE (RRID:SCR_012085) Copy   

•   Source: SciCrunch Registry

http://sketchel.sourceforge.net/

An interactive chemical molecule sketching tool, and molecular spreadsheet data entry application.

Proper citation: SketchEl (RRID:SCR_012082) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/hopemap/

A connected-components based fast algorithm for network alignment.

Proper citation: HopeMap (RRID:SCR_012081) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mcdl/

A small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation.

Proper citation: MCDL (RRID:SCR_012084) Copy   

•   Source: SciCrunch Registry

http://glare.sourceforge.net/

A software that facilitates and improves the design of chemical combinatorial libraries.

Proper citation: GLARE (RRID:SCR_012083) Copy   

•   Source: SciCrunch Registry