MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences
Related Experiment Video
Updated: Aug 19, 2026

A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
James J Campanella1, Ledion Bitincka, John Smalley
1Montclair State University, Department of Biology and Molecular Biology, 1 Normal Avenue, Montclair, New Jersey 07043 USA. james.campanella@montclair.edu
Background:
The rapid increase in the amount of protein and DNA sequence information available has become almost overwhelming to researchers. So much information is now accessible that high-quality, functional gene analysis and categorization has become a major goal for many laboratories. To aid in this categorization, there is a need for non-commercial software that is able to both align sequences and also calculate pairwise levels of similarity/identity.
Results:
We have developed MatGAT (Matrix Global Alignment Tool), a simple, easy to use computer application that generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data.
Conclusions:
The advantages of this program over other software are that it is open-source freeware, can analyze a large number of sequences simultaneously, can visualize both sequence alignment and similarity/identity values concurrently, employs global alignment in calculations, and has been formatted to run under both the Unix and the Microsoft Windows Operating Systems. We are presently completing the Macintosh-based version of the program.
Related Concept Videos
Evolutionary Relationships through Genome Comparisons
MALDI-TOF Mass Spectrometry
Peptide Identification Using Tandem Mass Spectrometry
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
Proteomics
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Modern Molecular Taxonomy
Applications of Molecular Taxonomy

