# Clustal Omega - convert from distance into # of substitutions

I have a set of nucleotide sequences for which I have aligned using Clustal Omega. In particular, I performed a full alignment, and obtained a full distance matrix.

The distance matrix scores range between 0 and 1. I am looking to use this score to back-compute the number of different positions present in the alignment. Is this possible? If possible, I'm looking to avoid using code (my own or otherwise) to re-compute the number of positions differing between each pair of segments, and instead compute it directly from the distance score.

Here is a toy example of what I am receiving from ClustalOmega:

Sequence    1    2    3    4
1           0    0.1  0.06 0.1
2                0    0.4  0.23
3                     0    0.05
4                          0


The numbers are the "distances" as calculated by ClustalOmega. According to the README file, they are computed by the k-tuple measure. I tried parsing the original paper (published in 1983 in PNAS), but I could not figure out how k-tuple distances are computed, and I could not figure out how the distance metric (as reported like above) is computed from k-tuple distances.

I would like to convert those numbers into the number of positions that differ between each pair of sequences when the two are aligned. This includes substitutions, insertions, deletions. I am currently doing this for 520 sets of virus sequences. Is this possible?

• What exactly do you mean by "positions" in your alignment? How many sequences are we talking about? Can you show an example of the matrix and your desired result? Commented Mar 24, 2014 at 19:56
• Sure, let me update the original question. Commented Mar 24, 2014 at 22:36
• It uses a gonet matrix to compare each of these two sequences. Since you you could have insertions and extensions as well as substitutions, it becomes a 3 parameter problem. 1*open + 6*penalty + substituion_penalty = X. X can be solved by a linear combination of subsituion_penalties, extensions, and insertions. So I think this will be really really hard. Commented Mar 25, 2014 at 8:21
• with that being said. Clustal spits out the multiple sequence alightment. Why don't you just look at sequence 1 and sequence 2 and see what the insertions and subtitutions are! Commented Mar 25, 2014 at 8:22
• Haha, it looks like I will have to do that in the end. I was trying to see if I could take the lazy route and not write a few lines of code. Thank you for all of your input nonetheless! Commented Mar 25, 2014 at 13:00