Purdue University

MILC represents part of a set of codes written by the MIMD Lattice Computation MILC collaboration used to study quantum chromodynamics QCD, the theory of the strong interactions of subatomic physics. It performs simulations of four dimensional SU3 lattice gauge theory on MIMD parallel machines. Strong interactions are responsible for binding quarks into protons and neutrons and holding them all together in the atomic nucleus.

Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads.

Miniasm is a very fast OLC-based de novo assembler for noisy long reads.

Minimap2 is a versatile pairwise aligner for genomic and spliced nucleotide sequences.

Minipolish is a tool for Racon polishing of miniasm assemblies.

Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Miniprot is similar to GeneWise and Exonerate in functionality but it can map proteins to whole genomes and is much faster at the residue alignment step.

miRDeep2 discovers active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, ...).

Mirtop is a ommand line tool to annotate with a standard naming miRNAs e isomiRs.

Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.

Mlst is used to scan contig files against traditional PubMLST typing schemes.

Mmseqs2 is a software suite to search and cluster huge protein and nucleotide sequence sets.

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.

Modbam2bed is a program to aggregate modified base counts stored in a modified-base BAM file to a bedMethyl file.

Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology.

ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces.

ModuleTree or modtree helps users naviagate between different application stacks and sets up a default compiler and mpi environment.

momi (MOran Models for Inference) is a Python package that computes the expected sample frequency spectrum (SFS), a statistic commonly used in population genetics, and uses it to fit demographic history

System resource monitoring tool.

Mothur is an open source software package for bioinformatics data processing. The package is frequently used in the analysis of DNA from uncultured microbes.

Motif - Graphical user interface GUI specification and the widget toolkit.