Jaya, for me it is working perfectly.

@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");
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output:

CH7     0       1
1CP5    1       2
1LHT    2       3
1SPG    3       4
1FAW    4       5
1HBR    5       6
1WMU    6       7
1F5P    7       8
1UC3    8       9
3LHB    9       10
1IT2    10      11
9 -2393.2 (((1,2),3),4,5,6,7)))),((8,10),9),11)
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