MatGAT (Matrix Global Alignment Tool) 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.
Data may be input into MatGAT as a cut and paste function or using a browse function for larger files. Files must be plain text in the standard FASTA format with multiple sequence analysis if each has a FASTA title line starting with ">". Files of up to 100 DNA or protein sequences have been analyzed successfully using MatGAT. The user may specify which type of alignment matrix (BLOSUM, PAM, etc.) he may want to employ with his DNA or protein sequences.
MatGATv2.01 now is able to directly transfer results over to MS Excel and create a spreadsheet with a single button command.
(bug fix 03/11/04 - Improper sequences alignment, if the combined length of a pair of sequences is larger than 12,000 characters. Only the alignment of these pair sequences is affected. The alignment of any other pair sequences whose combine length is less than 12,000 is NOT affected, eventhough they may be aligned in a session that contains one or more pairs of sequences whose combined length exceeds 12,000)
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