Clustal Omega - Convert From Distance Into # Of Substitutions

Question

[ericmajinglong]

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.

Answer 1

[Joseph Hughes]

I believe Clustalo provides uncorrected pairwise distances, so you can multiply your distance by the length of the sequence to obtain the number of differences between two sequences.