#!/usr/bin/perl -w

use Bio::TreeIO;

my $usage="Usage: $0 [-hn] [treeFile ...]\n".
 " -n: input is in newick (phylip) format: default = nexus (paup*) format\n";

use Getopt::Std;
my %opts=();
getopts('hb:n',\%opts) || die "$usage\n";

die "$usage\n" if ($opts{h});

@ARGV = ('-') unless @ARGV;  # take STDIN when no arg.

my $treeOut = Bio::TreeIO->new('-format' => 'lintree', 'file' => '>-');

my $infile;
while ($infile = shift @ARGV) {
    my $inFormat = ($opts{n}) ? 'newick' : 'nexus';
    my $treeIN = new Bio::TreeIO(-file => $infile, -format => $inFormat);

    my $cntr = 1;
    while (my $tree = $treeIN->next_tree) {
	
	$treeOut->write_tree($tree);
    }
}

exit(0);