Answers.Body: <p>It works for me with the <a href="http://darlinglab.org/mauve/download.html" rel="nofollow noreferrer">download from download page</a>. The download archive contains <code>Mauve.jar</code> so the command line in the answer you link to should work.</p>
  
  <p>However, you might need to include all the jar files (not just <code>Mauve.jar</code>) in the classpath for this to command work, though. For instance, the following works for me:</p>
  
  <pre class="lang-bash prettyprint-override"><code>MAUVE_DIR=‹the-dir-containing-Mauve.jar›
  export CLASSPATH="$(find "$MAUVE_DIR" -name \*.jar -print0 | tr '\0' :)$CLASSPATH"
  java org.gel.mauve.analysis.SnpExporter -f aln.xmfa -o aln.snps
  </code></pre>
  
  <p>… there’s probably a smarter way to make this work but I don’t use Java enough to know how.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-02-28T16:35:38.540Z
Answers.Text: Should I download this file: http://darlinglab.org/mauve/snapshots/2015/2015-02-25/MacOS/Mauve-snapshot_2015-02-25.dmg ? But this is to install mauve, right? Where can I find the Mauve.jar file?
Answers.UserDisplayName: Biomagician
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-02-28T16:40:06.600Z
Answers.Text: @charlesdarwin macOS applications are *regular directories*. Open the DMG and go inside the `Mauve.app` dir. Inside that directory you’ll find `/Contents/Java/Mauve.jar`; to display the contents in Finder, use the instructions here: https://apple.stackexchange.com/a/95942/2392 — but in the terminal you can simply `cd` into the directory.
Answers.UserDisplayName: Konrad Rudolph
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-02-28T11:11:23.110Z
Answers.LastActivityDate: 2018-02-28T11:11:23.110Z
Answers.UserDisplayName: Konrad Rudolph
Body: <p>I am using <a href="http://darlinglab.org/mauve/" rel="nofollow noreferrer">Mauve</a> to align two whole genomes. I use the following command to get the alignment in xmfa format:</p>
  
  <p><code>/Applications/Mauve.app/Contents/MacOS/progressiveMauve ref1.fa ref2.fa --output alignment.xmfa</code></p>
  
  <p>I then open the xmfa file in the Mauve GUI and export the SNPs. Is there a way of doing this using a command? I have tried to follow the procedure described <a href="https://sourceforge.net/p/mauve/mailman/message/31871278/" rel="nofollow noreferrer">here</a> but the <a href="http://gel.ahabs.wisc.edu/mauve/snapshots" rel="nofollow noreferrer">link</a> to snapshot releases of Mauve does not work anymore.</p>
  
  <p>I could not find anything in the Mauve command line help:</p>
  
  <p><code>/Applications/Mauve.app/Contents/MacOS/progressiveMauve --help</code></p>
  
  <p>nor on the <a href="http://darlinglab.org/mauve/" rel="nofollow noreferrer">Mauve website</a>.</p>
  
  <p>I tried the procedure described by Konrad Rudolph. I wrote:</p>
  
  <p>MAUVE_DIR=/Applications/Mauve.app/Contents/Java</p>
  
  <p>in the terminal. Is this correct? Don't I need an export and quotation marks to create a bash variable? I tried adding an export and using quotation marks for the file but the error below remained the same.</p>
  
  <p>followed by:</p>
  
  <p><code>export CLASSPATH="$(find "$MAUVE_DIR" -name \*.jar -print0 | tr '\0' :)$CLASSPATH"</code></p>
  
  <p>followed by:</p>
  
  <p>java org.gel.mauve.analysis.SnpExporter -f alignment.xmfa -o aln.snps</p>
  
  <p>and it seems to work.</p>
  
Tags: <phylogenetics><snp><variation><mauve>
Title: Can I export the SNPs between whole genome alignments using the command line?
ThreadText: # Can I export the SNPs between whole genome alignments using the command line?
  
  (Asked by: username_0 on 2018-02-28)
  
  I am using [Mauve](http://darlinglab.org/mauve/) to align two whole genomes. I use the following command to get the alignment in xmfa format:
  
  `/Applications/Mauve.app/Contents/MacOS/progressiveMauve ref1.fa ref2.fa --output alignment.xmfa`
  
  I then open the xmfa file in the Mauve GUI and export the SNPs. Is there a way of doing this using a command? I have tried to follow the procedure described [here](https://sourceforge.net/p/mauve/mailman/message/31871278/) but the [link](http://gel.ahabs.wisc.edu/mauve/snapshots) to snapshot releases of Mauve does not work anymore.
  
  I could not find anything in the Mauve command line help:
  
  `/Applications/Mauve.app/Contents/MacOS/progressiveMauve --help`
  
  nor on the [Mauve website](http://darlinglab.org/mauve/).
  
  I tried the procedure described by username_1 username_1. I wrote:
  
  MAUVE\_DIR=/Applications/Mauve.app/Contents/Java
  
  in the terminal. Is this correct? Don't I need an export and quotation marks to create a bash variable? I tried adding an export and using quotation marks for the file but the error below remained the same.
  
  followed by:
  
  `export CLASSPATH="$(find "$MAUVE_DIR" -name \*.jar -print0 | tr '\0' :)$CLASSPATH"`
  
  followed by:
  
  java org.gel.mauve.analysis.SnpExporter -f alignment.xmfa -o aln.snps
  
  and it seems to work.
  
  **Tags:** phylogenetics, snp, variation, mauve
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-02-28. Score: 2 | Accepted answer
  
  It works for me with the [download from download page](http://darlinglab.org/mauve/download.html). The download archive contains `Mauve.jar` so the command line in the answer you link to should work.
  
  However, you might need to include all the jar files (not just `Mauve.jar`) in the classpath for this to command work, though. For instance, the following works for me:
  
  ```bash
  MAUVE_DIR=‹the-dir-containing-Mauve.jar›
  export CLASSPATH="$(find "$MAUVE_DIR" -name \*.jar -print0 | tr '\0' :)$CLASSPATH"
  java org.gel.mauve.analysis.SnpExporter -f aln.xmfa -o aln.snps
  
  ```
  
  … there’s probably a smarter way to make this work but I don’t use Java enough to know how.
  
  > **Comments:**
  > **username_0**: Should I download this file: http://darlinglab.org/mauve/snapshots/2015/2015-02-25/MacOS/Mauve-snapshot_2015-02-25.dmg ? But this is to install mauve, right? Where can I find the Mauve.jar file?  
  > **username_1**: @charlesdarwin macOS applications are *regular directories*. Open the DMG and go inside the `Mauve.app` dir. Inside that directory you’ll find `/Contents/Java/Mauve.jar`; to display the contents in Finder, use the instructions here: https://apple.stackexchange.com/a/95942/2392 — but in the terminal you can simply `cd` into the directory.  
  
  ---
  
  