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.
Follow these steps to install a support package.
In the Environment section of the MATLAB toolstrip, select Add-Ons > Get Add-Ons.
In the Add-On Explorer, search for the support package that you want to install by entering its name.
Install the support package.
The following table lists all the Bioinformatics Toolbox support packages that are available for download as Add-Ons.
Support Package Name
Corresponding MATLAB functions
Bioinformatics Toolbox Interface for Bowtie Aligner 
Mac and UNIX®
Cufflinks Support Package for the Bioinformatics Toolbox 
Mac and UNIX
Mac and UNIX
†Version of the original (third-party) software
 Langmead, Ben, and Steven L Salzberg. “Fast Gapped-Read Alignment with Bowtie 2.” Nature Methods 9, no. 4 (April 2012): 357–59. https://doi.org/10.1038/nmeth.1923.
 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.
 Mortazavi, Ali, Brian A Williams, Kenneth McCue, Lorian Schaeffer, and Barbara Wold. “Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq.” Nature Methods 5, no. 7 (July 2008): 621–28. https://doi.org/10.1038/nmeth.1226.
 Li, Heng, and Richard Durbin. “Fast and Accurate Long-Read Alignment with Burrows–Wheeler Transform.” Bioinformatics 26, no. 5 (March 1, 2010): 589–95. https://doi.org/10.1093/bioinformatics/btp698.
 Li, Heng, and Richard Durbin. “Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform.” Bioinformatics 25, no. 14 (July 15, 2009): 1754–60. https://doi.org/10.1093/bioinformatics/btp324.