Purdue University

MACS2 is Model-based Analysis of ChIP-Seq for identifying transcript factor binding sites.

MACS3 is Model-based Analysis of ChIP-Seq for identifying transcript factor.

MAFFT is a multiple alignment program for amino acid or nucleotide sequences.

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.

MAKER is a popular genome annotation pipeline for both prokaryotic and eukaryotic genomes. This guide describes best practices for running MAKER on RCAC clusters.

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.

Mapcaller is an efficient and versatile approach for short-read mapping and variant identification using high-throughput sequenced data.

mapDamage2 is a computational framework written in Python and R, which tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

MarginPolish is a graph-based assembly polisher. It iteratively finds multiple probable alignment paths for run-length-encoded reads and uses these to generate a refined sequence. It takes as input a FASTA assembly and an indexed BAM (ONT reads aligned to the assembly), and it produces a polished FASTA assembly.

Mash is a fast sequence distance estimator that uses MinHash.

Mashmap is a fast approximate aligner for long DNA sequences.

Mashtree is a tool to create a tree using Mash distances.

The MaSuRCA (Maryland Super Read Cabog Assembler) genome assembly and analysis toolkit contains of MaSuRCA genome assembler, QuORUM error corrector for Illumina data, POLCA genome polishing software, Chromosome scaffolder, jellyfish mer counter, and MUMmer aligner.

Mathematica is a technical computing environment and programming language with strong symbolic and numerical abilities.

MATLAB MATrix LABoratory is a multi-paradigm numerical computing environment and fourth-generation programming language. A proprietary programming language developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, C#, Java, Fortran and Python.

Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.

Maxbin2 is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.

Maxquant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.

Mcl is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs.

The MCScanX package has two major components: a modified version of MCscan algorithm allowing users to handle MCScan more conveniently and to view multiple alignment of syntenic blocks more clearly, and a variety of downstream analysis tools to conduct different biological analyses based on the synteny data generated by the modified MCScan algorithm.