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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 outfile, outfile.backbone and output.bbcols.

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.

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mauve documentation have a similar command but the usage is --id-matrix=<file>. So very similar to the progressivemauve command (just doesn't include --input). Try it and see if it works.

I think it's a bug for sure as several other people on biostar have complained.

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It indeed seems that the --input-id-matrix option doesn't work as expected, as Amar has pointed out.

I tried the following command:

./progressiveMauve genome1.fasta genome2.fasta genome3.fasta --output=test > test.log

And saw the following bits in test.log (truncated):

[...]
Genome conservation distance matrix:
0       0.0767545       0.187454
0.0767545       0       0.193385
0.187454        0.193385        0

[...]
genome content distance matrix:
0       0.0767545       0.187454
0.0767545       0       0.193385
0.187454        0.193385        0

bp distance matrix:
0.9     0.0125  0.075
0.0125  0.9     0.0375
0.075   0.0375  0.9
[...]

Could any of those three tables contain the information you are looking for?

p.s. as an aside, if you are looking into a way to obtain a whole genome similarity matrix you might want to look into mash or sourmash.

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