Please forgive us should this question is similar to someone else's: How to generate identity matrix files using Mauve?
We were trying to make a genome comparison analysis using progressiveMauve of S. aureus contig in multiFASTA format from several strains (approx. 2.9 mbps each) produced from SPAdes assembly. We tried to generate identity percentage matrix using progressiveMauve by typing in --input-id-matrix command as it was documented from the manual, however the program acted as if it doesn't recognize such command (instead of error message, the screen showed as if --version was typed).
Was it there something wrong with the data type or the progressiveMauve itself? Please assist. Thank you beforehands.