Dear Dr. Gilbert, I am submitting a software package called MatGAT (Matrix Global Alignment Tool) to the Indiana Biology software archive. The attached software was written by one of my students, Ledion Bitincka. The program is also available for distribution at my own laboratory website, but we wanted to allow for a larger distribution from the IUBIO Archive. MatGAT is a simple, easy to use similarity/identity matrix generator. It calculates the similarity and identity between every pair of DNA or protein sequences in a given data set without needing pre-alignment of the data. The program performs a series of pairwise alignments, calculates similarity and identity, and then places the results in a distance matrix that can be directly transferred to MS Excel for further analysis. It is an ideal tool for use in phylogenomic analyses. The attached zipped version of MatGAT runs on the Windows 98, NT, 2000, and XP OS's . We have completed a Unix version of the software and are finishing development on a Mac OS X version. We will submit these in the future. I thank you for your help. Sincerely, Jim Campanella Professor Montclair State University Dept. of Biology and Molecular Biology Montclair, NJ 07043