text: user10365: 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.
  
  user3848: 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
  
  user10365: 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
  
original_text: 10365: <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>
   3848: <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>
   10365: <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>
  