I am using Mauve to compare multiple genomes. On the mannual page http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-output-file-formats.html, the author said an identity matrix file of the genomes compared could be generated.

However, under command-line condition, I couldn't generate this file at all with command like this:

mauveAligner --output=test.mauve --output-alignment=test.alignment --id-matrix=test.id.matrix.txt ...

Anybody knows how to generate this file?

Thanks!