Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-19T12:00:42.817Z
Answers.LastActivityDate: 2019-07-19T12:00:42.817Z
Answers.UserDisplayName: M__
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-01-28T01:46:19.450Z
Answers.LastActivityDate: 2021-01-28T01:46:19.450Z
Answers.UserDisplayName: undress
Body: <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>
  
Tags: <phylogenetics><multiple-sequence-alignment><sequence-alignment>
Title: Differences in webtool and standalone Clustal Omega Percent Identity Matrix
ThreadText: # 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
  
  
  ---
  
  