M

http://liulab.dfci.harvard.edu/MACS/

Model Based Analysis for ChIP-Seq data

Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform

a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology

NCBI BLAST next generation read mapper

MAKER is a portable and easily configurable genome annotation pipeline.

Structural variant and indel caller for mapped sequencing data

mapDamage: tracking and quantifying damage patterns in ancient DNA sequences http://geogenetics.ku.dk/all_literature/mapdamage/

This package provides an implementation of the inference pipeline of MassiveFold v1.0.0, based on AlphaFold2

MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software. MaSuRCA requires Illumina data, and supports third-generation PacBio/Nanopore MinION reads for hybrid assembly.

a desktop environment tuned for iterative analysis and design processes with a programming language that expresses matrix and array mathematics directly

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

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

Meta-pipeline to identify transposable element insertions using next generation sequencing data

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

Neural network sequence error correction.

MEGAHIT: An ultra-fast single-node solution for large and complex

Nanopore modified base and sequence variant detection.

A tool for studying the taxonomic content of a set of DNA reads

Motif based sequence Analysis tools

Mercat: a versatile counter and diversity estimator for data base independent property analysis obtained from whole community sequencing data.

Evaluate genome assemblies with k-mers and more Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a set of tools for this purpose.

Metagenome binning

A scalable high-throughput metabolic and biogeochemical functional trait profiler.

A workflow for marine Genomic Observatories' data analysis

a graphical binning tool that makes use of multivariate statistics of tetranucleotide frequencies and differential coverage based binning

MetaWRAP is a pipeline for genome-resolved metagenomic data analysis

MGLTools is an program for visualization and analisys of molecular structures.

An integrated pipeline for estimating strain-level genomic variation from metagenomic data

Population Genetics - Panmixia and Migration detection

MindTheGap performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome. MindTheGap can also be used as a genome assembly finishing tool, it can fill the gaps between a set of input contigs without any a priori on their relative order and orientation.

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

A versatile pairwise aligner for genomic and spliced nucleotide sequences.

A tool for Racon polishing of miniasm assemblies

miR-PREFeR: microRNA PREdiction From small RNAseq data

MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads)

A completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs

mitochondrial baiting and iterative mapping

A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes.

MMseqs2.0: ultra fast and sensitive sequence search and clustering suite

ModelAngelo is an automatic atomic model building program for cryo-EM maps.

A bioinformatics tool for working with modified bases from Oxford Nanopore

Evolutionary inference using SFS and LD statistics.

Automatic Molecular Replacement Pipeline

Fast BAM/CRAM depth calculation for WGS, exome, or targetted sequencing.

a program for integrating single crystal diffraction data from area detectors

This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

Correction of electron beam-induced sample motion is one of the major factors contributing to the recent resolution breakthroughs in cryo-electron microscopy

Marker gene-based OTU (mOTU) profiling

Bayesian Inference of Phylogeny

Population genetics simulator

Create aggregate bioinformatics analysis reports across many samples and tools

MUMmer is a system for rapidly aligning entire genomes

MUSCLE: multiple sequence alignment with high accuracy and high throughput

MUltiScale enrIchment Calling for ChIP-Seq Datasets

Multivariate regression trees

tool to automatically quantify pathological features in muscle fiber histology images

MySQL client applications and tools