[Bioperl-l] phylogeny-trait association methods into BioPerl

Heikki Lehvaslaiho heikki at sanbi.ac.za
Fri Sep 19 12:22:23 EDT 2008


The code is now in SVN. Bio::Tree::TreeFunctionsI::add_trait() can be used to 
set trait values in a tree.

Enjoy,

   -Heikki

On Wednesday 10 September 2008 13:32:06 Heikki Lehvaslaiho wrote:
> FYI,
>
> I've been recently writing code to analyse phylogeny-trait associations.
> These traits are typically geographical location of the sequence but they
> can be any phenotypic characters associated with the sequences.
>
> This involves trees, i.e. Bio::Tree::Tree and Bio::Tree::Node objects and
> strings describing the traits. I've been using tags to store trait values
> within nodes. The tag methods are:
>
> Bio::Tree::Node::add_tag_value
> Bio::Tree::Node::get_all_tags
> Bio::Tree::Node::get_tag_values
> Bio::Tree::Node::has_tag
> Bio::Tree::Node::remove_all_tags
> Bio::Tree::Node::remove_tag
>
> Question: Is  there any particular reason why there is no
> set_tag_value(scalar|@array) method?
>
> I am getting tired of writing:
>   $node->remove_tag($key);
>   map {$node->add_tag_value($key)} @values ;
> so I am going to implement that unless there is are strong objections.
>
> Otherwise it has been smooth sailing. I am going to add
> Bio::Tree::TreeFunctions::is_binary() and start populating
> Bio::Tree::Statistics soon with these methods:
>
> ps() - Parsimony Score (PS) from Fitch 1971
> ai() - Association index (AI) of Whang et al. 2001
> mc() - Monophyletic Clade (MC) size statistics by Salemi at al. 2005
> cherries() - number of leaf node pairs
>
> If you have any comments, please feel free to post them here.
>
>     -Heikki

-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________



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