calculation of polimorphism matrix (P-distance)
Distance matrix procedure: distance_matrix_P-dist.awk Average distance matrix procedure: P-dist_av.awk Example aligned sequences: sequences.aln Output matrix: sequences_P-dist.mtr
Execute procedure of distance matrix (gawk should be installed):
gawk -f distance_matrix_P-dist.awk name_1=NG37 size=14 sequences.aln > sequences_P-dist.mtr
Parameters: name_1 - referal genome size - minimal number alined sequences
Calulation of average mean of each matrix: Parameters: mingene=N (minimal number of genes)
gawk -f P-dist_av.awk sequences_P-dist.mtr > sequences_P-dist.tab