Hi Thomas, Yes you are very true. So I have edited the code properly this time and introduces proper variable names and indentation. 
#This program read the triplets from file named "data" and returns the
#supertree. 
# ___DATA(triplets)____
#b c a
#a c d
#d e b
#### NOTE ::: SuperTree part hasnt been incorporated yet.
use strict;
use warnings;
use Data::Dumper;
use Graph; 
use Data::Dump qw/ pp /;
####READ IN THE INPUT DATA ########
my @triplets; # Get all the triplets
 while (<>) {
        push @triplets, [ split ];
    }

#Make a deep copy of @triplets 
my @triplet_deep_copy = map { [@$_] } @triplets;


#####AUXILIARY GRAPH   G(L) #######
# In order to generate the G(L)  first of all extract first two column
+s of  @triplets into another matrix
my @auxiliary_edges=@triplets;
splice(@$_, 2, 1)
foreach @auxiliary_edges;
print "----EDGE LIST TO BUILD AUXILIARY GRAPH-----\n";
print Dumper \@auxiliary_edges;


##### CONNECTED COMPONENTS ##########
my $auxiliary_graph = Graph->new( undirected => 1 );

my @from;
my @to;
for (my $p = 0; $p <= 2; $p++) {
        $from[$p]=$triplets[$p][0];
  }

for (my $q = 0; $q <= 2; $q++) {
        $to[$q]=$triplets[$q][1];
  }

for (my $r = 0; $r <= 2; $r++) {
     $auxiliary_graph->add_edge($from[$r], $to[$r]);
 }

my @subgraphs = $auxiliary_graph->connected_components; # Subgraphs
my $V = $auxiliary_graph->vertices; # Number of taxa
my $connected_components=scalar @subgraphs; #Get the number of connect
+ed components

###### FINDING THE TRIPLETS WHICH ARE SUBSET(OR INDUCED BY) OF EACH OF
+ THE CONNECTED COMPONENTS######
Main(@auxiliary_edges);
exit(0);
sub induced {
  my $trip = shift;
  my @matches;
  for my $QT ( @_ ) {
         for my $triplet ( @$trip ) {
                my %seen;        # my %Pie;
                undef @seen{@$QT};
                delete @seen{@$triplet};
                if ( keys( %seen ) <= ( @$QT - @$triplet ) ) {
                     push @matches, $triplet;
      }
    } ## end for my $triplet ( @$trip )
  } ## end for my $QT ( @_ )
  return @matches;
}## end sub induced


sub Main {
  my $tree = Graph->new( undirected => 1 );
  my $dad='u';
  $tree->add_vertex($dad);
  for my $one (@subgraphs) {
      my @matches = induced( \@triplet_deep_copy, $one );
      print "\nTriplet induced by subgraph ", pp( $one => { MATCHES =>
+ \@matches } ), "\n\n";
  }
}

[download]

In reply to Re^2: supertree construction in perl by zing
in thread supertree construction in perl by zing

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.