[Bioperl-l] proposal: CDAT (character data and trees) integrative object

Arlin Stoltzfus stoltzfu at umbi.umd.edu
Tue May 9 16:22:43 EDT 2006


Dear developers--

We propose a Bio::CDAT (Character Data And Trees) module to  
facilitate comparative analysis
using evolutionary methods by 1) managing evolutionary relationships  
(by linking data to trees)
and 2) allowing coordinated analysis of different types of data (by  
implementing a generic concept
of “character-state” data).

Bio::CDAT would take advantage of existing BioPerl objects and would  
include the functionality
of Rutger Vos's Bio::Phylo.  It would provide the framework to  
develop interfaces to analysis tools
(phylogeny inference, evolutionary rate models, functional shift  
inference, etc), as well as to file
formats and visualization methods appropriate for such analyses.

A proposal is attached.  We would like to hear your thoughts (e.g.,  
see the section on "Questions
to consider")!  Thanks

Arlin Stoltzfus
WeiGang Qiu
Rutger Vos
(with thanks to Justin Reese and Aaron Mackey)
------------------
Arlin Stoltzfus (stoltzfu at umbi.umd.edu)
CARB, 9600 Gudelsky Drive, Rockville, Maryland  20850
tel 240 314 6208, fax 240 314 6255, www.molevol.org/camel
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