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

Heikki Lehvaslaiho heikki at sanbi.ac.za
Wed Sep 10 07:32:06 EDT 2008


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

-- 
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      _/      _/
     _/  _/  _/  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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