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Hi greengaroo, The algorithm is this:- Pictorial representation:- http://picpaste.com/triplets-IQMFT1QY.jpg
Triplets :: S=('b,c|a', 'a,c|d', 'd,e|b'), Species :: L={a,b,c,d,e} TreeConstruct(S): 1.] Let L be the set of species in S. Build G(L) the auxillary graph. 2.] Let C1,C2....Cq be the set of connected components in G(L). 3.] If q>1,then - For i=1,2.....q, let S(i) be the set of triplets in S labeled by +the set of leaves in C(i). - Let T(i) = TreeConstruct(S(i)) - Let T be a tree formed by connecting all T(i) with the same paren +t node. Return T. 4.]If q=1 & C1 contains exactly one leaf,return the leaf ,else return +fail.
I have updated the code and now it takes input connections in form of triplets and prints the connected components of the graph.
use strict; use warnings; use Graph; @ARGV = ('b,c|a', 'a,c|d', 'd,e|b') unless @ARGV; my %HoA; foreach ( @ARGV ) { m/^([a-z])[,]([a-z])[|]([a-z])$/ ; push @{$HoA{$1}}, $2; } print "\n===========\@HoA=====\n"; print "from->to\n"; while (my ($key, $values) = each %HoA) { print $key, "=> [", join(',', @$values), "]\n"; } my $g = Graph->new( undirected => 1 ); for my $src ( keys %HoA ) { for my $tgt ( @{ $HoA{$src} } ) { $g->add_edge($src, $tgt); } } my @subgraphs = $g->connected_components; my @allgraphs; for my $subgraph ( @subgraphs ) { push @allgraphs, {}; for my $node ( @$subgraph ) { if ( exists $HoA{ $node } ) { $allgraphs[-1]{$node} = [ @{ $HoA{$node} } ]; } } } print "----connected components------------"; use YAML; print Dump \@allgraphs; -------------OUTPUT---------------- ===========@HoA===== from->to a=> [c] b=> [c] d=> [e] ----connected components--------------- - a: - c b: - c - d: - e
Hope this helps you get an idea

In reply to Re^2: phylogenetic tree construction using perl by zing
in thread phylogenetic tree construction using perl by zing

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