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https://hci-bio-app.hci.utah.edu/gnomex/

A Genomic Laboratory Information Management System (LIMS) and Data repository that can function as an experiment tracking and workflow management system for Core Facilities as well as an advanced data repository for storing and sharing genomic data sets.

Proper citation: GNomEx (RRID:SCR_011805) Copy   

•   Source: SciCrunch Registry
  

http://www.jcvi.org/metarep/

A tool for high-performance comparative metagenomics that allows users to view, query, browse, and compare metagenomics annotation profiles from short reads or assemblies. Users can use statistical tests, hierarchical clustering, multidimensional scaling, and heat maps to compare multiple datasets at various functional and taxonomic levels.

Proper citation: METAREP (RRID:SCR_011926) Copy   

•   Source: SciCrunch Registry
  

http://infernal.janelia.org/

Software for searching DNA sequence databases for RNA structure and sequence similarities.

Proper citation: Infernal (RRID:SCR_011809) Copy   

•   Source: SciCrunch Registry
  

http://www.ncbi.nlm.nih.gov/blast/html/megablast.html

Software that uses the greedy algorithm for nucleotide sequence alignment search.

Proper citation: Mega BLAST (RRID:SCR_011920) Copy   

•   Source: SciCrunch Registry
  

http://www.ige.tohoku.ac.jp/joho/gmProject/gmhome.html

A graphical interface for comparative genomics.

Proper citation: GenomeMatcher (RRID:SCR_011800) Copy   

•   Source: SciCrunch Registry
  

http://drive5.com/usearch/manual/uclust_algo.html

Algorithm that divides a set of sequences into clusters

Proper citation: UCLUST algorithm (RRID:SCR_011921) Copy   

•   Source: SciCrunch Registry
  

http://www-ps.informatik.uni-tuebingen.de/itNew/?page_id=1160

Alignment visualization based on SuperGenome coordinates.

Proper citation: GenomeRing (RRID:SCR_011801) Copy   

•   Source: SciCrunch Registry
  

http://www.che.udel.edu/eXPatGen/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A simulator of gene expression patterns in order to evaluate different analysis methods, such as clustering and principle component analysis (PCA).

Proper citation: eXPatGen (RRID:SCR_011922) Copy   

•   Source: SciCrunch Registry
  

http://try-gobe.appspot.com/

An interactive, web-based tool for comparative genomic visualization.

Proper citation: Gobe (RRID:SCR_011802) Copy   

•   Source: SciCrunch Registry
  

http://cas-bioinfo.cas.unt.edu/gsv/homepage.php

Software that allows users to upload files which contain synteny regions between two or more genomes and interactively visualize the synteny between them.

Proper citation: GSV (RRID:SCR_011803) Copy   

•   Source: SciCrunch Registry
  

https://www.softgenetics.com/NextGENe.php

Software tool for Next Generation sequence analysis. Analytical partner for analysis of desktop sequencing data produced by Illumina iSeq, Miniseq, MiSeq, NextSeq, HiSeq, and NovaSeq systems, Ion Torrent Ion GeneStudio S5, PGM, and Proton systems as well as other platforms. Software runs on Windows Operating System, which provides biologist friendly interface. It does not require scripting or other bioinformatics support.

Proper citation: NextGENe (RRID:SCR_011859) Copy   

•   Source: SciCrunch Registry
  

http://www.uwi.edu/

Originally University College of the West Indies, is a public university system.

Proper citation: University of the West Indies; Kingston; Jamaica (RRID:SCR_011730) Copy   

•   Source: SciCrunch Registry
  

http://www.csd.uwo.ca/~ilie/RACER/

A software program for correcting errors in sequencing data.

Proper citation: RACER (RRID:SCR_011852) Copy   

•   Source: SciCrunch Registry
  

http://www.utoronto.ca/

Public research university in Toronto, Ontario, Canada, located on the grounds that surround Queen's Park.

Proper citation: University of Toronto; Ontario; Canada (RRID:SCR_011733) Copy   

•   Source: SciCrunch Registry
  

http://www.unitn.it/en

Italian university located in Trento and nearby Rovereto. It has been able to achieve considerable results in didactics, research, and international relations according to CENSIS and the Italian Ministry of Education.

Proper citation: University of Trento; Trento; Italy (RRID:SCR_011734) Copy   

•   Source: SciCrunch Registry
  

http://cbio.ensmp.fr/~ahaury/svn/dream5/html/index.html

Software providing a scoring technique for stability selection, which improves the performance of feature selection with LARS. TIGRESS can be run online through the GenePattern platform (GP-DREAM, http://dream.broadinstitute.org).

Proper citation: TIGRESS (RRID:SCR_011977) Copy   

•   Source: SciCrunch Registry
  

http://www.utwente.nl/en/

Public technical university located in Enschede, the Netherlands.

Proper citation: University of Twente; Overijssel; Netherlands (RRID:SCR_011737) Copy   

•   Source: SciCrunch Registry
  

https://trac.nbic.nl/narwhal/

Automates the primary analysis of massive parallel sequencing data.

Proper citation: NARWHAL (RRID:SCR_011858) Copy   

•   Source: SciCrunch Registry
  

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

A software tool for high speed estimation of homology relations within and between species in massive data sets.

Proper citation: orthAgogue (RRID:SCR_011979) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/apps/mediawiki/seqgene/?title=SeqGene

An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc.

Proper citation: SeqGene (RRID:SCR_011861) Copy   

•   Source: SciCrunch Registry