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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

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.csd.uwo.ca/~ilie/RACER/

A software program for correcting errors in sequencing data.

Proper citation: RACER (RRID:SCR_011852) 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

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   

•   Source: SciCrunch Registry

https://github.com/MikkelSchubert/adapterremoval

Software program to remove residual adapter sequences from next generation sequencing reads. Used for cleaning of next-generation sequencing reads. AdapterRemoval v2 introduces improvements in throughput, through use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support; handles datasets containing reads or read-pairs with different adapters or adapter pairs; provides simultaneous demultiplexing and adapter trimming; has ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets; provides native gzip and bzip2 support.

Proper citation: AdapterRemoval (RRID:SCR_011834) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry