I'm just getting started with the Mauve aligner and I'm finding the documentation a bit lacking. I'm using the
progressiveMauve tool from the command line and would like to output an identity matrix file. The set of output files it generates by default for
progressiveMauve --output=outfile are
The documentation for the tool lists an
--input-id-matrix option but this doesn't seem to have any effect. The documentation page for output files does describe an identity matrix file but doesn't say anything about how to generate it.