Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-01T11:52:11.200Z
Answers.LastActivityDate: 2017-06-01T11:52:11.200Z
Answers.UserDisplayName: Ammar
Answers.Body: <p>It indeed seems that the <code>--input-id-matrix</code> option doesn't work as expected, as <a href="https://bioinformatics.stackexchange.com/a/346/123">Amar has pointed out</a>.</p>
  
  <p>I tried the following command:</p>
  
  <pre><code>./progressiveMauve genome1.fasta genome2.fasta genome3.fasta --output=test &gt; test.log
  </code></pre>
  
  <p>And saw the following bits in <code>test.log</code> (truncated):</p>
  
  <pre><code>[...]
  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
  [...]
  </code></pre>
  
  <p>Could any of those three tables contain the information you are looking for?</p>
  
  <p>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 <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x" rel="nofollow noreferrer">mash</a> or <a href="https://sourmash.readthedocs.io/en/latest/" rel="nofollow noreferrer">sourmash</a>.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-31T09:18:38.437Z
Answers.LastActivityDate: 2017-08-31T09:18:38.437Z
Answers.UserDisplayName: mgalardini
Body: <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>
  
Tags: <phylogenetics>
Title: How can I output an identity matrix in progressiveMauve?
ThreadText: # How can I output an identity matrix in progressiveMauve?
  
  (Asked by: username_0 on 2017-05-29)
  
  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](http://darlinglab.org/mauve/user-guide/progressivemauve.html) for the tool lists an `--input-id-matrix` option but this doesn't seem to have any effect. The [documentation page for output files](http://darlinglab.org/mauve/user-guide/files.html) does describe an identity matrix file but doesn't say anything about how to generate it.
  
  **Tags:** phylogenetics
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2017-06-01. Score: 1
  
  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.
  
  
  ---
  
  ### Answer by username_2 on 2017-08-31. Score: 0
  
  It indeed seems that the `--input-id-matrix` option doesn't work as expected, as [Amar has pointed out](https://bioinformatics.stackexchange.com/a/346/123).
  
  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](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x) or [sourmash](https://sourmash.readthedocs.io/en/latest/).
  
  
  ---
  
  