Hello! Does anyone know of a script or programme to build a matrix based on alignment of 2 or more proteins? I would like to have something like a table where for each amino acid or gap in row there is a number of how many times it changed to the one in column. Thank you in advance
So I made a replacement dictionary as described in one of the answers here: Creating your own substitution matrix from an alignment and then on its base I built a matrix where the substitutions like A->T and Y->A are counted as separate. Because SubsMat module seems to only allow you to build symmetrical matrices where the direction of change doesn't count.