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https://github.com/nicolazzie/AffyPipe
An open-source software pipeline for Affymetrix Axiom genotyping workflow.
Proper citation: AffyPipe (RRID:SCR_002032) Copy
https://github.com/adrlar/CanSNPer
Software that is a hierarchical genotype classifier of clonal pathogens.
Proper citation: CanSNPer (RRID:SCR_001980) Copy
http://sourceforge.net/projects/denovoassembler/files/
Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2.
Proper citation: Ray (RRID:SCR_001916) Copy
http://cakesomatic.sourceforge.net/
A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.
Proper citation: Cake (RRID:SCR_002133) Copy
https://github.com/mpyatkov/sbars
Bioinformatics tool for searching different types of long repeats in sequences comparable by size with chromosomes.
Proper citation: SBARS (RRID:SCR_002371) Copy
http://www.bioconductor.org/packages/release/bioc/html/CAMERA.html
A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data.
Proper citation: CAMERA - Collection of annotation related methods for mass spectrometry data (RRID:SCR_002466) Copy
http://droog.gs.washington.edu/polyphred/
Software program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. Its functions are integrated with the use of three other programs: Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool.
Proper citation: PolyPhred (RRID:SCR_002337) Copy
http://cran.r-project.org/web/packages/isa2/
A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix.
Proper citation: Iterative Signature Algorithm (RRID:SCR_002327) Copy
Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: FATCAT (RRID:SCR_014631) Copy
https://gemini.readthedocs.io/en/latest/
Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.
Proper citation: GEMINI (RRID:SCR_014819) Copy
https://omics.pnl.gov/software/ms-gf
Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
Proper citation: MS-GF+ (RRID:SCR_015646) Copy
http://www.ebi.ac.uk/Tools/msa/kalign/
A fast and accurate multiple sequence alignment algorithm.
Proper citation: Kalign (RRID:SCR_011810) Copy
http://wishart.biology.ualberta.ca/cgview/
A Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CGView (RRID:SCR_011779) Copy
http://bioen-compbio.bioen.illinois.edu/PSAR-Align/
Software for improving multiple sequence alignment using probabilistic sampling.
Proper citation: PSAR-Align (RRID:SCR_011814) Copy
http://gaggle.systemsbiology.net/docs/geese/genomebrowser/
An open source software tool for visualizing high-density data plotted against coordinates on the genome.
Proper citation: Gaggle (RRID:SCR_011780) Copy
https://bioinf.eva.mpg.de/patman/
Software that searches for short patterns in large DNA databases, allowing for approximate matches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PatMaN (RRID:SCR_011821) Copy
Software for searching DNA sequence databases for RNA structure and sequence similarities.
Proper citation: Infernal (RRID:SCR_011809) Copy
http://utgenome.org/index.html
An open-source software for developing personalized genome browsers that work in web browsers.
Proper citation: UTGB Toolkit (RRID:SCR_011797) Copy
http://graphics.med.yale.edu/trim/
A fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines.
Proper citation: Btrim (RRID:SCR_011836) Copy
http://www.genome.umd.edu/quorum.html
Software tool as error corrector for Illumina reads. It is distributed and used with MaSuRCA, or it can be used independently.
Proper citation: QuorUM (RRID:SCR_011840) Copy
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