Tools   Select Another Resource Report Type

http://seqtracs.sourceforge.net/

Software for a Laboratory Information Management System (LIMS) for tracking, organizing, and accessing sequencing requests and ABI trace files produced by a centralized sequencing core facility.

Proper citation: SeqTRACS (RRID:SCR_013294) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/crossbow/index.shtml

A scalable software pipeline for whole genome resequencing analysis.

Proper citation: Crossbow (RRID:SCR_013306) Copy   

•   Source: SciCrunch Registry

http://tomcatbackup.esat.kuleuven.be/inclusive/

A suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.

Proper citation: INCLUSive (RRID:SCR_013488) Copy   

•   Source: SciCrunch Registry

http://ctb.pku.edu.cn/main/SheGroup/Software/MED2.htm

A non-supervised gene prediction algorithm for prokaryotic genomes with multivariate entropy distance method.

Proper citation: MED (RRID:SCR_013403) Copy   

•   Source: SciCrunch Registry

http://hannonlab.cshl.edu/Alta-Cyclic/main.html

An Illumina Genome-Analyzer (Solexa) base caller.

Proper citation: Alta-Cyclic (RRID:SCR_013373) Copy   

•   Source: SciCrunch Registry

http://www.cisd.ethz.ch/software/openBIS

Software for an open, distributed system for managing biological information that supports biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. The openBIS software framework can be easily extended and has been customized for the following technologies: * High Content Screening * Proteomics * Deep Sequencing * Metabolomics

Proper citation: openBIS (RRID:SCR_011815) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/msa/kalign/

A fast and accurate multiple sequence alignment algorithm.

Proper citation: Kalign (RRID:SCR_011810) Copy   

•   Source: SciCrunch Registry

http://mafft.cbrc.jp/alignment/server/

Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.

Proper citation: MAFFT (RRID:SCR_011811) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Accurate error correction in high-throughput sequencing data.

Proper citation: HiTEC (RRID:SCR_011826) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://bix.ucsd.edu/projects/hammer/

A tool for error correction of short read datasets with non-uniform coverage, such as single-cell data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Hammer (RRID:SCR_011825) Copy   

•   Source: SciCrunch Registry

http://www.g-language.org/GenomeProjector/

A searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk.

Proper citation: Genome Projector (RRID:SCR_011790) Copy   

•   Source: SciCrunch Registry

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

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

Proper citation: Gobe (RRID:SCR_011802) Copy   

•   Source: SciCrunch Registry