<p>Try clustal omega, instead of clustalw because it is really old. It should report to 2 dp. Variations do occur depending on how indels are treated, but this is just rounding.</p>

<p>You could try </p>

<pre><code>alignment -tree -pim -score
</code></pre>

<p>The idea is to convert to absolute rather than percentage and might overcome the rounding error</p>

CC BY-SA 4.0
2019-07-19T12:00:42.817Z
2019-07-19T12:00:42.817Z
M__
<p>So, after a year I came out with the solution - as M__ kindly suggested, using Clustal Omega.</p>
<p>First, align usign muscle:</p>
<p><code>muscle -in fasta -quiet -out alignment</code></p>
<p>Then, generate percent distance matrix using clustal omega:</p>
<p><code>clustalo --infile alignment --distmat-out output --percent-id --full</code></p>

CC BY-SA 4.0
2021-01-28T01:46:19.450Z
2021-01-28T01:46:19.450Z
undress
<p>I'm trying to align sequences using MUSCLE in my own computer. To compute Percent Identity Matrix I'm trying to use Clustal2.1 like it's done in <a href="https://www.ebi.ac.uk/Tools/msa/muscle/" rel="nofollow noreferrer">https://www.ebi.ac.uk/Tools/msa/muscle/</a>. Even though I'm doing the same thing, I get rounded up values in my computer. </p>

<p>For example, this is the webtool output:</p>

<pre><code>#
#
#  Percent Identity  Matrix - created by Clustal2.1 
#
#

     1: JX310755.1  100.00   92.79   65.29   63.98
     2: M97264.1     92.79  100.00   65.66   63.92
     3: AJ292230.1   65.29   65.66  100.00   66.88
     4: KM379144.1   63.98   63.92   66.88  100.00
</code></pre>

<p>And this is the output in my computer.</p>

<pre><code>#
#
#  Percent Identity  Matrix - created by Clustal2.1 
#
#

     1: JX310755.1     100      93      65      64
     2: M97264.1        93     100      66      64
     3: AJ292230.1      65      66     100      67
     4: KM379144.1      64      64      67     100
</code></pre>

<p>I have both installed clustalw using <code>sudo apt install clustalw</code> and by downloading the tarballs from <a href="http://www.clustal.org/download/current/clustalw-2.1.tar.gz" rel="nofollow noreferrer">http://www.clustal.org/download/current/clustalw-2.1.tar.gz</a>, with exact results. </p>

<p>The commmand I'm using is <code>clustalw2 alignment -tree -pim</code>.</p>

<p>Any thoughts on why this could be? Thanks in advance.</p>

<phylogenetics><multiple-sequence-alignment><sequence-alignment>
Differences in webtool and standalone Clustal Omega Percent Identity Matrix
# Differences in webtool and standalone Clustal Omega Percent Identity Matrix

(Asked by: username_0 on 2019-07-19)

I'm trying to align sequences using MUSCLE in my own computer. To compute Percent Identity Matrix I'm trying to use Clustal2.1 like it's done in https://www.ebi.ac.uk/Tools/msa/muscle/. Even though I'm doing the same thing, I get rounded up values in my computer. 
For example, this is the webtool output:
#
#
#  Percent Identity  Matrix - created by Clustal2.1 
#
#

     1: JX310755.1  100.00   92.79   65.29   63.98
     2: M97264.1     92.79  100.00   65.66   63.92
     3: AJ292230.1   65.29   65.66  100.00   66.88
     4: KM379144.1   63.98   63.92   66.88  100.00

And this is the output in my computer.
#
#
#  Percent Identity  Matrix - created by Clustal2.1 
#
#

     1: JX310755.1     100      93      65      64
     2: M97264.1        93     100      66      64
     3: AJ292230.1      65      66     100      67
     4: KM379144.1      64      64      67     100

I have both installed clustalw using sudo apt install clustalw and by downloading the tarballs from http://www.clustal.org/download/current/clustalw-2.1.tar.gz, with exact results. 
The commmand I'm using is clustalw2 alignment -tree -pim.
Any thoughts on why this could be? Thanks in advance.

**Tags:** phylogenetics, multiple-sequence-alignment, sequence-alignment

---

## 2 answers

### Answer by username_0 on 2021-01-28. Score: 2 | Accepted answer

So, after a year I came out with the solution - as M\_\_ kindly suggested, using Clustal Omega.

First, align usign muscle:

`muscle -in fasta -quiet -out alignment`

Then, generate percent distance matrix using clustal omega:

`clustalo --infile alignment --distmat-out output --percent-id --full`


---

### Answer by username_1 on 2019-07-19. Score: 2

Try clustal omega, instead of clustalw because it is really old. It should report to 2 dp. Variations do occur depending on how indels are treated, but this is just rounding.
You could try 
alignment -tree -pim -score

The idea is to convert to absolute rather than percentage and might overcome the rounding error


---

