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.


UnRar is a utility for extracting WinRar archives (.rar files).

Globus Command Line Interface

Globus is a data transfer service designed for convenient, fast file transferes between computer systems. More information about using Globus on MSI can be found here.  These command line tools provide an alternative interface to the Globus functionality.


Phobius is "a combined transmembrane topology and signal peptide predictor". 


Funannotate is a pipeline for genome annotation originally designed for use with fungi genomes, but it can also be applied for other eukaryotes.


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


RNAmmer is software for predicting ribosomal RNA in full gene sequences.

To use this program at MSI, please send a a request to help@msi.umn.edu and ask to be added to the RNAmmer group. The use of RNAmmer at MSI is limited to academic researchers.


TMHMM is software for the prediction of transmembrane helices in proteins.


To use this program at MSI, please send a a request to help@msi.umn.edu and ask to be added to the TMHMM group. The use of TMHMM at MSI is limited to academic researchers.


BRAKER1 is software for unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS.