[Phylobase-devl] iEvoBio presentation about phylobase

Hilmar Lapp hlapp at nescent.org
Wed Apr 16 23:30:45 CEST 2014

Great to see this presented at iEvoBio!


On Wed, Apr 16, 2014 at 3:56 PM, François Michonneau <
francois.michonneau at gmail.com> wrote:

> 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).
>   cheers,
>   -- François
> *Title*
> phylobase: an R package for associating, manipulating and plotting
> phylogenetic trees and comparative data
> *Abstract*
> 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 to:
>    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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Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io
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