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."