<p>I’ve seen cases like this. For me, there were plasmids at end that didn’t get aligned.</p>

CC BY-SA 4.0
2023-09-06T14:41:22.973Z
Hi @SethCommichaux please do remember to provide supporting information for your answer, i.e. not simply to confirm the OP's observation but offer a solution.
M__
CC BY-SA 4.0
2022-03-14T20:40:54.483Z
Your answer could be improved with additional supporting information. Please [edit] to add further details, such as citations or documentation, so that others can confirm that your answer is correct. You can find more information on how to write good answers [in the help center](/help/how-to-answer).
Community
CC BY-SA 4.0
2022-03-14T20:40:20.363Z
2022-03-14T20:40:20.363Z
Seth Commichaux
<p>I am aligning 4 genomes of <em>Psuedomonas chlororaphis</em> using progressive mauve software. Command used:</p>
<pre><code>progressiveMauve --output=outputfile --disable-backbone chl189.fas chl17415.fas chl50083.fas chlTAMOak81.fas
</code></pre>
<p>At the end, the resulting aligned genomes are not of the same length. What could be the potential problems?</p>
<p><a href="https://i.sstatic.net/sfV99.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/sfV99.png" alt="enter image description here" /></a></p>
<p>This is a global alignment. Which is why im surprised that they aren't all the same length after alignment?
Also, while analysing the subsequent genomes, I noticed that some region which were present in only 2/4 genomes were misaligned in the end result. How do I proceed troubleshooting this problem?</p>
<p>I am a student and new to this field, could you please tell me how to proceed with manually checking to see whats wrong?</p>

<phylogenetics><genome><mauve>
What does it mean if aligned genomes are not of the same length?
# What does it mean if aligned genomes are not of the same length?

(Asked by: username_0 on 2020-05-01)

I am aligning 4 genomes of Psuedomonas chlororaphis using progressive mauve software. Command used:
progressiveMauve --output=outputfile --disable-backbone chl189.fas chl17415.fas chl50083.fas chlTAMOak81.fas

At the end, the resulting aligned genomes are not of the same length. What could be the potential problems?

This is a global alignment. Which is why im surprised that they aren't all the same length after alignment?
Also, while analysing the subsequent genomes, I noticed that some region which were present in only 2/4 genomes were misaligned in the end result. How do I proceed troubleshooting this problem?
I am a student and new to this field, could you please tell me how to proceed with manually checking to see whats wrong?

**Tags:** phylogenetics, genome, mauve

---

## 1 answers

### Answer by username_1 on 2022-03-14. Score: 1

I’ve seen cases like this. For me, there were plasmids at end that didn’t get aligned.

> **Comments:**
> **username_3**: Your answer could be improved with additional supporting information. Please [edit] to add further details, such as citations or documentation, so that others can confirm that your answer is correct. You can find more information on how to write good answers [in the help center](/help/how-to-answer).  
> **username_2**: Hi @SethCommichaux please do remember to provide supporting information for your answer, i.e. not simply to confirm the OP's observation but offer a solution.  

---

