[Phylobase-devl] iEvoBio presentation about phylobase

François Michonneau francois.michonneau at gmail.com
Wed Apr 16 21:56:10 CEST 2014

Hello all,

  I wanted to let you that I submitted an abstract for the iEvoBio
conference (http://ievobio.org/) where I intend to give a "lightening talk"
on phylobase. Let me know if you have any questions or feedback (I can edit
the abstract until midnight EDT tonight).

  -- François


phylobase: an R package for associating, manipulating and plotting
phylogenetic trees and comparative data


phylobase is an R package that provides S4 classes and methods to access
and manipulate phylogenetic objects, as well as associate data to
phylogenetic objects for comparative analysis. phylobase comes with methods

   1. describe phylogenetic objects (e.g., number of tips and edges, is the
   tree ultrametric?);
   2. annotate phylogenetic objects (nodes, edges and the entire object can
   be annotated);
   3. update properties of phylogenetic objects (e.g., change edge lengths);
   4. plot trees and associated data;
   5. query relationships among nodes (e.g., what are the
   ancestors/descendants of a given node?);
   6. subset phylogenetic objects (by specifying internal nodes and/or tips
   that should be included or excluded).

The package comes with S4 classes ensuring that the data structure is
robust, and the overhead associated with checking the validity of the
objects is limited by using C++ code. phylobase makes use of the NCL
library for reading NEXUS and Newick files. Over 250 unit tests are used to
maintain the integrity and compatibility of the methods during development.
phylobase intends to provide an intuitive, robust and efficient interface
to complex objects, and is ideally suited to develop packages for
phylogenetic and comparative analyses.
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