JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.
LASTZ is a program for aligning DNA sequences, a pairwise aligner.
Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants.
A probabilistic framework for structural variant discovery.
MACS does Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa).
MAFFT is a multiple sequence alignment program.
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.
MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecule sequencing (SMRT) reads.