Differences in webtool and standalone Clustal Omega Percent Identity Matrix 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.
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