#!/usr/bin/perl
use strict;
use warnings;

# FIND THE PATH TO THE Directory:
 my $dir = $ARGV[0];
 opendir(DIR, $dir) or die $!;
# select for files with names containing txt.fit 
my @files= grep { /txt.fit/ } readdir DIR;
 closedir DIR;

# Read files line by line
foreach my $file(@files) {
 open IN, "<$file" or die $!;
 my $tree = ();
 while(<IN>) {
# skip everything in file not conatining Tree mixture
   next unless ($_ =~ m/Tree mixture/);
# remove content from line thats unwanted in output
   $tree = $_;
   $tree =~s/Tree mixtureTree=//;
}
#name output file after input file but add .tre
my $outfile = "$file.tre";
# here i 'open' the file, saying i want to write to it with the '>>' symbol
open (FILE, ">> $outfile") || die "problem opening $outfile\n";
print FILE $tree;

}