<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>

CC BY-SA 3.0
2017-06-01T11:52:11.200Z
2017-06-01T11:52:11.200Z
Ammar
<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>

CC BY-SA 3.0
2017-08-31T09:18:38.437Z
2017-08-31T09:18:38.437Z
mgalardini
<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>

<phylogenetics>
How can I output an identity matrix in progressiveMauve?
# 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=`. 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.
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.


---

