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?