Hello-
I would like to produce a pairwise percent identity matrix between all
genomes aligned in progressiveMauve. I noticed the 2004-02-19 bug fix
report, where it says that the --id-matrix or -t command line options will
print out an identity matrix. However, when I use these switches, I get an
"invalid option" error. I assume this was implemented in mauveAligner and
not progressiveMauve. Is there a way to output the identity matrix in
progressiveMauve?
I noticed that the progressiveMauve algorithm produces a "genome content
distance matrix" at the beginning of the run, calculated for the initial set
of local multiple alignments. Does progressiveMauve compute another genome
content distance matrix based on the final alignment? Would such a matrix
be equivalent to a percent identity matrix?
Thanks for your help,
Matthew Bendall
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