#!/usr/bin/perl
use strict;
my $infile=$ARGV[0];
my $outfile=$infile;$outfile=~s/mafft/stockholm/;

my %id_seq;

open(IN,$infile)||die;
my $firstline=<IN>;$firstline=~/^>(.+)/;my $id=$1;my $seq;
while(my $line=<IN>){
	if($line=~/^>/){
		$id_seq{$id}=$seq;
		$line=~/^>(.+)/;
		$id=$1;
		$seq="";
	}else{
		chomp $line;
		$seq.=$line;
	}
}
close IN;
$id_seq{$id}=$seq;

open(OUT,">$outfile")||die;
foreach my $id(sort{$a cmp $b} keys %id_seq){
	print OUT sprintf("%-15s",$id).$id_seq{$id}."\n";
}
close OUT;