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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?

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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? –  terdon Mar 24 at 19:56
Sure, let me update the original question. –  ericmjl Mar 24 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. –  jwillis0720 Mar 25 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! –  jwillis0720 Mar 25 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! –  ericmjl Mar 25 at 13:00

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