run_phylip.pl

#!/usr/bin/perl -w                                                                                                                                                                                               
# run_phylip.pl                                                                                                                                                                                                  
use strict;

my $program = shift;
my $command = shift;
my $outfile = shift;
my $outtree = shift;

$program && $command && $outfile
  || die "Usage: ./run_phylip.pl program command_file output_file [output_tree]\n";

# get rid of previous work                                                                                                                                                                                       
unlink "infile"  if -e "infile";
unlink "intree"  if -e "intree";
unlink "outtree" if -e "outtree";
unlink "outfile" if -e "outfile";

# run the specified program with command file                                                                                                                                                                    
system "$program < $command > $program.out";
system "mv outfile $outfile";
system "mv outtree $outtree" if $outtree;

print "Done. Outfile saved as $outfile. Program output saved as '$program.out'\n";