@name = qw (CH7 1CP5 1LHT 1SPG 1FAW 1HBR 1WMU 1F5P 1UC3 3LHB 1IT2); 
$phylo = "9 -2393.2 (((CH7,1CP5),1LHT),1SPG,1FAW,1HBR,1WMU)))),((1F5P,3LHB),1UC3),1IT2)"; 

  for($i = 0,my $k = 1; $i<= $#name; ++$i,++$k){
    print "$name[$i]\t$i\t$k\n";
    $phylo =~ s/($name[$i])/$k/;
  }
  print("$phylo\n");