[Bioperl-l] Bio::Tools::Run::Phylo::Phyml, tree_string

[Tristan Lefebure]

Hi there,
I am not quite sure I understand why tree_string() from Bio::Tools::Run::Phylo::Phyml returns 
a string that looks like that (I removed the end of the tree):

Tree is BIONJ(((((((('92':0.0114354726,'12':0.0472591023)0.0000000000:0.0000005859,...

Why do we have this 'Tree is BIONJ' thing?

A quick look at the code in the _run() function gives :

	{
	open(my $FH_TREE, "<", $tree_file)
	    || $self->throw("Phyml call ($command) did not give an output: $?");
	local $/;
	$self->{_tree} .= <$FH_TREE>;
    }

Why appending something to $self->{_tree}? What about?
	$self->{_tree} = <$FH_TREE>;

I was about to fill a bug report, but then I saw that in Phyml.t:

    is substr($factory->tree_string, 0, 9), 'BIONJ(SIN', 'tree_string()';

Well, I am lost. Any help much appreciated...

--
Tristan