text: user126: 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.
  
  user490: 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. 
  
original_text: 126: <p>I'm just getting started with the Mauve aligner and I'm finding the documentation a bit lacking. I'm using the <code>progressiveMauve</code> tool from the command line and would like to output an identity matrix file. The set of output files it generates by default for <code>progressiveMauve --output=outfile</code> are <code>outfile</code>, <code>outfile.backbone</code> and <code>output.bbcols</code>.</p>
  
  <p>The <a href="http://darlinglab.org/mauve/user-guide/progressivemauve.html" rel="noreferrer">documentation</a> for the tool lists an <code>--input-id-matrix</code> option but this doesn't seem to have any effect. The <a href="http://darlinglab.org/mauve/user-guide/files.html" rel="noreferrer">documentation page for output files</a> does describe an identity matrix file but doesn't say anything about how to generate it.</p>
   490: <p>mauve documentation have a similar command but the usage is <code>--id-matrix=&lt;file&gt;</code>. So very similar to the progressivemauve command (just doesn't include --input). Try it and see if it works. </p>
  
  <p>I think it's a bug for sure as several other people on biostar have complained. </p>
  