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Bioinformatics Toolbox Software Support Packages

Bioinformatics Toolbox™ provides support packages for various next-generation sequencing workflows and analyses. To make a support package available in your MATLAB® command line, you must first install it.

Install Support Package

Follow these steps to install a support package.

  1. In the Environment section of the MATLAB toolstrip, select Add-Ons > Get Add-Ons.

  2. In the Add-On Explorer, search for the support package that you want to install by entering its name.

  3. Install the support package.

For details about installing add-ons, see Get and Manage Add-Ons. For other information, see Add-Ons.

Available Support Packages

The following table lists all the Bioinformatics Toolbox support packages that are available for download as Add-Ons.

Support Package Name


Corresponding MATLAB functions

Supported OS

Bowtie 2 Support Package for Bioinformatics Toolbox [1] (download link)


bowtie2, bowtie2build, bowtie2inspect.

Windows®, Mac, and Linux®

Cufflinks Support Package for the Bioinformatics Toolbox [2] (download link)


cufflinks, cuffcompare, cuffdiff, cuffgffread, cuffgtf2sam, cuffmerge, cuffnorm, cuffquant.

Windows, Mac, and Linux

BWA Support Package for Bioinformatics Toolbox [3][4] (download link)


bwaindex, bwamem.

Windows, Mac, and Linux

SRA Toolkit for Bioinformatics Toolbox [5] (download link)


srafasterqdump, srasamdump

Windows, Mac, and Linux

BLAST+ Support Package for Bioinformatics Toolbox [6][7] (download link)


blastplusdatabase, blastplus, blastplusoptions

Windows, Mac, and Linux

Version of the original (third-party) software

You need to install Windows Subsystem for Linux (WSL) and a Linux distribution on your Windows machine. For details on installing WSL, see here.

Related Topics


[1] Langmead, Ben, and Steven L Salzberg. “Fast Gapped-Read Alignment with Bowtie 2.” Nature Methods 9, no. 4 (April 2012): 357–59.

[2] Trapnell, Cole, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, and Lior Pachter. “Transcript Assembly and Quantification by RNA-Seq Reveals Unannotated Transcripts and Isoform Switching during Cell Differentiation.” Nature Biotechnology 28, no. 5 (May 2010): 511–15.

[3] Li, Heng, and Richard Durbin. “Fast and Accurate Long-Read Alignment with Burrows–Wheeler Transform.” Bioinformatics 26, no. 5 (March 1, 2010): 589–95.

[4] Li, Heng, and Richard Durbin. “Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform.” Bioinformatics 25, no. 14 (July 15, 2009): 1754–60.

[6] Camacho, Christiam, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, and Thomas L Madden. “BLAST+: Architecture and Applications.” BMC Bioinformatics 10, no. 1 (December 2009): 421.

[7] “BLAST: Basic Local Alignment Search Tool.”