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http://tvap.genome.wustl.edu/tools/music/
A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MuSiC (RRID:SCR_008792) 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://code.google.com/p/edmr/
Comprehensive differentially methylated regions (DMR) analysis based on bimodal normal distribution model and weighted cost function for regional methylation analysis optimization.
Proper citation: eDMR (RRID:SCR_006960) Copy
https://github.com/steinmann/peakzilla
An algorithm to identify transcription factor binding sites from ChIP-seq data.
Proper citation: Peakzilla (RRID:SCR_007471) Copy
https://code.google.com/p/ampliconnoise/
A collection of programs for the removal of noise from 454 sequenced PCR amplicons. This project also includes the Perseus algorithm for chimera removal.
Proper citation: AmpliconNoise (RRID:SCR_007814) 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
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://code.google.com/p/cutadapt/
Software tool that removes adapter sequences from DNA sequencing reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: cutadapt (RRID:SCR_011841) Copy
http://genopole.pasteur.fr/SynTView/
An interactive multi-view genome browser for next-generation comparative microorganism genomics.
Proper citation: SynTView (RRID:SCR_011939) Copy
http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php
A Next-Generation Sequencing Simulator for Metagenomics.
Proper citation: NeSSM (RRID:SCR_011941) Copy
http://metavelvet.dna.bio.keio.ac.jp/
Software for a short read de novo metagenome assembly created by modifying and extending a single-genome and de Bruijn-graph based assembler, Velvet.
Proper citation: MetaVelvet (RRID:SCR_011915) Copy
http://omics.informatics.indiana.edu/GeneStitch/
Network Matching Algorithm using the de Bruijn graph assembly of metagenomes to improve the assembly of genes.
Proper citation: GeneStitch (RRID:SCR_011910) Copy
http://bayescall.sourceforge.net/
An efficient model-based base-calling algorithm for high-throughput sequencing.
Proper citation: naiveBayesCall (RRID:SCR_011866) Copy
http://pages.cs.wisc.edu/~bsettles/abner/
A software tool for molecular biology text analysis. At ABNER''s core is a statistical machine learning system using linear-chain conditional random fields (CRFs) with a variety of orthographic and contextual features.
Proper citation: ABNER (RRID:SCR_011868) Copy
http://transcriptome.ens.fr/eoulsan/
A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers.
Proper citation: Eoulsan (RRID:SCR_011901) Copy
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