#!/bin/sh

#This script does Clustal Omega alignment for listed sequences in files.
#You should have one list of files with listed sequences in the same directory as files.
#You should install Clustal Omega before running script.

FILES=./hb_seq/*

for file in $FILES
do
	filename=$(basename "$file")
	clustalo -i ${file} -o ./hb_ali/"${filename}".txt -v --outfmt=fa

done

