Clustalw

#!/bin/sh
argv=$1
clustalw <<!
1
./$argv
2
1



X
X
!

~/bin/clustalw2 -infile=$i -outfile=$outfile -output=fasta > $outfile2;

clustalw2 parameters http://anthrax.zlog.cn/17215.html

or use MUSCLE

~/bin/src/muscle/muscle -in $i -out $outfile -stable -quiet