[Bioperl-l] Bio::Tree method - FixedTopo tree factory with random branchlengths

Albert Vilella avilella at gmail.com
Mon Sep 19 07:00:38 EDT 2005


I am looking to implement a method for a Bio::Tree object that will
generate a number of trees with the same topology as the input tree
but with random branch lengths for each branch given.

I would like to ask where do you think is the best place to implement
this: RandomFactory.pm ? Maybe this should go inside
DistanceFactory ? Maybe put in another module.

My idea is that one would call the method with something similar to

my $treeio = new Bio::TreeIO(-format => 'newick', -file =>
my $tree = $treeio->next_tree;
my $out = Bio::TreeIO->new
     -format => 'newick',
     -file   => ">$outfile"
my $factory = new Bio::Tree::RandomFactory(
        -tree => $tree,
        -maxcount => $maxcount,
        -method => "fixedtopo",

while(my $generatedtree = $factory->next_tree) {

There would be something like a "fixedtopo_maxlen" so that the random
lengths fall inside the (0..maxlen) range.

I would be glad to know how do you think this could be implemented, of
if there is an easier way to do so with the current methods.

Thanks in advance,


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