Use of such a great module was fundamental for a swift development of a few routines aiming at exporting a big number of newick trees as svg files, scaled and colored at will by the biologist.
A question on how to colorize the node names was answered (and solved) by Rudger Vos in less than 2 hours !!
I have only one word: "Many thanks for this great module"
This module has been fundamental for my work. Rutger Vos helped me very quickly to make my perl script works well especially for the ladderize or order functions which needs the use of Bio::Phylo::Factory module.
my $factory = Bio::Phylo::Factory->new(
'node' => 'Bio::Phylo::Forest::DrawNode',
'tree' => 'Bio::Phylo::Forest::DrawTree',
my $tree = parse(
'-format' => 'newick',
'-string' => $input,
'-factory' => $factory,
The result is exactly what I was expected.
Thanks for this tool and for your Help !!
I am happily using this package for quite some time and I am still surprised by it's flexibility and the variety build in subs. The author response fast to questions, hence there is nothing to complain. Very nice package, which should be keept alive and up-to-date.
Bio::Phylo is really a complete solution not only for phylogenetic manipulation, but serialization and analysis as well. The author's NeXML phylogenetic markup standard is fully integrated into Bio::Phylo, so that users will be able to transparently incorporate this emerging standard into their applications. BioPerl has also plugged into Bio::Phylo; BioPerlers interested in trying Bio::Phylo's NeXML capabilities will find an easy way into Bio::Phylo using the Bio::NexmlIO wrapper. The package is complex and thorough, this does give class navigation a steep learning curve. POD is complete and contains overviews, however. (Full disclosure: I have participated in Bio::Phylo development.)
I have been happily using this module for the last year. It allows me to read Newick tree files and draw pretty SVG trees that have a large number of branches (>1,000). It is quite excellent to have SVG output since it allows to easily customize the tree or plot additional information on top of it.
The author is very responsive and open to suggestions, so that's a plus!
Works great - very useful!
I am the author of Bio::Phylo. Thank you for your interest! Bio::Phylo is under active development. I hope you will find it useful for parsing, visualizing and transforming phylogenetic data.
1 hidden unhelpful review