Pairwise mismatch count from multifasta alignment

FastaToSNPCount.sh

#!/bin/bash

#########################################
# Anuj Sharma                           #
# rknx@outlook.com                      #
# 2022-10-13                            #
#########################################

# Usage: FastaToSNPCount.sh <input.fasta>

awk -vRS=">" -vFS="\n" -vOFS="\t" '
    { a[$1] = $2; next}
    END{
        for (i in a) {printf "\t%s", i}
        for (i in a){
            printf "\n%s", i;
            for (j in a) {
                mis=0
                for (k=1; k<length($2); k++){
                    if (substr(a[i], k, 1) != substr(a[j], k, 1)){ mis++ }
                }
                printf "\t%s", mis;
            }
        }
        print "";
    }
' $1

exit 0