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.
From the OrthoFinder website: Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"
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.
NOTE: MSI has discontinued its support of Lasergene software, and will be uninstalling it from all systems on January 26, 2018. MSI understands that you may have questions about this decision, which we have attempted to answer below. Why is MSI discontinuing Lasergene support? The Minnesota Supercomputing Institute seeks to provide researchers at the University of Minnesota access to high-performance computing resources and user support to facilitate successful and innovative research in all disciplines. While MSI recognizes that Lasergene is an important tool for many biology labs on campus...