QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline.


RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for post- analyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads.




FALCON and FALCON-Unzip provide algorithms to assemble Single Molecule Real-Time (SMRT(R)) Sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. 


Spliced Transcripts Alignment to a Reference (STAR) is a software package developed for aligning large RNA-seq datasets.


Trinotate is a transcriptome annotation suite designed for use with de novo assembled transcriptomes from model or non model organisms.


GeneMark is the name of a set of gene prediction programs developed at the Georgia Institure of Technology. Genemark-ET is a member of this set of software for semi-supervised analysis of novel genomes.

To use this program at MSI, please send a a request to and ask to be added to the GeneMark group. The use of GeneMark at MSI is limited to academic researchers.




Galaxy is a web-based platform for data intensive biomedical research.  Anyone with an account at MSI can access the Galaxy server at


Software which uses a clustering approach for identification of enriched domains from histone modification ChIP-Seq data.


"RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST+ suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler."

RNAz (DISABLED - will be removed 9/28/2017)

NOTE: Due to lack of use, this software module has been disabled and will be removed from MSI systems on 9/28/2017. If you need this software, please contact


"RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs."