Software List

MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

Model-based Analysis of ChIP-Seq (MACS), for identifying transcript factor binding sites.

MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc.

Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout

MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.

Maple is a symbolic mathematics program.

Model-based Analysis of Regulation of Gene Expression

MASS is a command-line program written in C to perform fixed-effects (FE) and random-effects (RE) meta-analysis of sequencing studies by combining the score statistics from multiple studies.

MaSuRCA is whole genome assembly software.

Mathematical and technical computing package.

The matio software contains a library for reading and writing MATLAB MAT files from C and C++ programs.

Matlab programming environment.

Matrix2png is a simple but powerful program for making visualizations of microarray data and many other data types.

Materials Studio is a complete modeling and simulation environment designed to predict and understand the relationships of a material’s atomic and molecular structure.

Mauve is a system for constructing multiple genome alignments

Maven is a software project management and comprehension tool

The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs.

MCNP is a Monte Carlo N-Particle code.

MCNP is a Monte Carlo N-Particle code.

The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components

Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems, along with our MPB eigenmode package.

MEGAHIT is a single node assembler for large and complex metagenomics NGS reads

MEME discovers novel, ungapped motifs in your sequences

MetaBAT, An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities

metaCRISPR is a tool to assemble CRISPRs

METAL is a tool for meta-analysis genomewide association scans.

Metaxa2: Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data

METIS – Serial Graph Partitioning and Fill-reducing Matrix Ordering

MinCED – Mining CRISPRs in Environmental Datasets

Includes the utilities: juliet, cleric and fuse

Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data.

PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics.

Intel optimized BLAS/LAPACK libraries, also including FFT and other mathematical and statistical routines.

Transcript and gene level expression analysis using multi-mapping RNA-seq reads

Molpro is a comprehensive system of ab initio programs for advanced molecular electronic structure calculations.

Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. It incorporates the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more.

MIT Photonic-Bands (MPB) package is a free program for computing the band structures (dispersion relations) and electromagnetic modes of periodic dielectric structures, on both serial and parallel computers.

MPI bindings for use within Python.

MPlayer is a movie player supporting many different video files and output drivers.

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.