A simple similarity/identity matrix generator in Java
MatGAT 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.
MatGAT performs a series of pair-wise 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.
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What's New in This Release:
- Fixes issues with MatGat 2.02 UNIX version: if the compilation and testing all went fine but during operation you get an error saying "More than one sequence needed for alignment", please add the align file that was created during the compilation into a directory that is contained in the path.