Latest update of MUMmer written by CBD Project Scientist
Aligning DNA sequences has been and remains one of the fundamental tool in computational biology. It is widely used to compare genomes, to find SNPs and genome variations, and as a step in many other bioinformatics pipelines.
MUMmer, a widely used alignment package in genomics, was originally published in 1999 when the number and the size of available genome sequences was still small. It has been updated a few times since and the third version MUMmer3 remains a very popular genome to genome aligner.
MUMmer4 is the latest update written by Guillaume Marçais, Project Scientist in the Carnegie Mellon Computational Biology Department. It is a backward compatible version with MUMmer3, while being more versatile, being able to handle much larger sequences and faster. MUMmer4 handles genome to genome comparison as well as aligning short and long reads to a reference genome.