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http://go.princeton.edu/cgi-bin/GOTermFinder

The Generic GO Term Finder finds the significant GO terms shared among a list of genes from an organism, displaying the results in a table and as a graph (showing the terms and their ancestry). The user may optionally provide background information or a custom gene association file or filter evidence codes. This tool is capable of batch processing multiple queries at once. GO::TermFinder comprises a set of object-oriented Perl modules GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script. This implementation, developed at the Lewis-Sigler Institute at Princeton, depends on the GO-TermFinder software written by Gavin Sherlock and Shuai Weng at Stanford University and the GO:View module written by Shuai Weng. It is made publicly available through the GMOD project. The full source code and documentation for GO:TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: Generic GO Term Finder (RRID:SCR_008870) Copy   

•   Source: SciCrunch Registry

http://plantgrn.noble.org/LegumeIP/

LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes. LegumeIP currently hosts large-scale genomics and transcriptomics data, including: * Genomic sequences of three model legumes, i.e. Medicago truncatula, Glycine max (soybean) and Lotus japonicus, including two reference plant species, Arabidopsis thaliana and Poplar trichocarpa, with the annotation based on UniProt TrEMBL, InterProScan, Gene Ontology and KEGG databases. LegumeIP covers a total 222,217 protein-coding gene sequences. * Large-scale gene expression data compiled from 104 array hybridizations from L. japonicas, 156 array hybridizations from M. truncatula gene atlas database, and 14 RNA-Seq-based gene expression profiles from G. max on different tissues including four common tissues: Nodule, Flower, Root and Leaf. * Systematic synteny analysis among M. truncatula, G. max, L. japonicus and A. thaliana. * Reconstruction of gene family and gene family-wide phylogenetic analysis across the five hosted species. LegumeIP features comprehensive search and visualization tools to enable the flexible query on gene annotation, gene family, synteny, relative abundance of gene expression.

Proper citation: LegumeIP (RRID:SCR_008906) Copy   

•   Source: SciCrunch Registry

http://www.igbam.bilgem.tubitak.gov.tr/softwares/HomSI/

A software tool that identifies homozygous regions using deep sequence data.

Proper citation: HomSI (RRID:SCR_010771) Copy   

•   Source: SciCrunch Registry

http://contra-cnv.sourceforge.net/

A tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.

Proper citation: CONTRA (RRID:SCR_010814) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/breseq/

A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data intended for haploid microbial genomes.

Proper citation: breseq (RRID:SCR_010810) Copy   

•   Source: SciCrunch Registry

http://mutpred.mutdb.org/

Web application tool developed to classify an amino acid substitution as disease-associated or neutral in human.

Proper citation: MutPred (RRID:SCR_010778) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/mutsig

Software that analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.

Proper citation: MutSig (RRID:SCR_010779) Copy   

•   Source: SciCrunch Registry

http://svdetect.sourceforge.net/Site/Home.html

Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads.

Proper citation: SVDetect (RRID:SCR_010812) Copy   

•   Source: SciCrunch Registry

http://snpanalyzer.uthsc.edu/

A tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) has a phenotypic effect.

Proper citation: nsSNPAnalyzer (RRID:SCR_010780) Copy   

•   Source: SciCrunch Registry

https://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational-

Software tool as whole genome shotgun assembler that can generate high quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers.

Proper citation: ALLPATHS-LG (RRID:SCR_010742) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/soapdenovo.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 24,2023. Software tool for de novo assembly of human genomes with massively parallel short read sequencing.Short-read assembly method that can build de novo draft assembly for human sized genomes.Software package for assembling short oligonucleotide into contigs and scaffolds., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPdenovo (RRID:SCR_010752) Copy   

•   Source: SciCrunch Registry

http://www.molecularevolution.org/software/genomics/velvet

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Velvet (RRID:SCR_010755) Copy   

•   Source: SciCrunch Registry

https://www.hgsc.bcm.edu/content/atlas2

A next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in WECS data.

Proper citation: Atlas2 (RRID:SCR_010756) Copy   

•   Source: SciCrunch Registry

http://berry.engin.umich.edu/oligoarray2_1/

A free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction.

Proper citation: OligoArray (RRID:SCR_010961) Copy   

•   Source: SciCrunch Registry

http://furlonglab.embl.de/methods/tools/coco

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2021.A computational tool that allows the user to search, visualise and store different data associated with gene expression.

Proper citation: CoCo (RRID:SCR_010947) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/limma/

Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.

Proper citation: LIMMA (RRID:SCR_010943) Copy   

•   Source: SciCrunch Registry

http://liulab.dfci.harvard.edu/NPS/

A python software package that can identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level.

Proper citation: NPS (RRID:SCR_010890) Copy   

•   Source: SciCrunch Registry

http://linus.nci.nih.gov/BRB-ArrayTools.html

An integrated software package for the visualization and statistical analysis of DNA microarray gene expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BRB-ArrayTools (RRID:SCR_010938) Copy   

•   Source: SciCrunch Registry

http://mmb.pcb.ub.es/nucleR/

A R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats.

Proper citation: nucleR (RRID:SCR_010895) Copy   

•   Source: SciCrunch Registry

http://genovar.sourceforge.net/

A Detection and Visualization software tool for Genomic Variants.

Proper citation: Genovar (RRID:SCR_010930) Copy   

•   Source: SciCrunch Registry