nlme, lattice, graphics, stats, tools, utils, parallel

ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Emmanuel Paradis [aut, cre, cph],
  Simon Blomberg [aut, cph],
  Ben Bolker [aut, cph],
  Julien Claude [aut, cph],
  Hoa Sien Cuong [aut, cph],
  Richard Desper [aut, cph],
  Gilles Didier [aut, cph],
  Benoit Durand [aut, cph],
  Julien Dutheil [aut, cph],
  Olivier Gascuel [aut, cph],
  Christoph Heibl [aut, cph],
  Daniel Lawson [aut, cph],
  Vincent Lefort [aut, cph],
  Pierre Legendre [aut, cph],
  Jim Lemon [aut, cph],
  Rosemary McCloskey [aut, cph],
  Johan Nylander [aut, cph],
  Rainer Opgen-Rhein [aut, cph],
  Andrei-Alin Popescu [aut, cph],
  Manuela Royer-Carenzi [aut, cph],
  Klaus Schliep [aut, cph],
  Korbinian Strimmer [aut, cph],
  Damien de Vienne [aut, cph]

Interface to BioMart databases (e.g. Ensembl, COSMIC ,Wormbase
and Gramene)

Steffen Durinck <durincks@gene.com>,
	Wolfgang Huber <huber@ebi.ac.uk>

Sean Davis <sdavis2@mail.nih.gov>, Francois Pepin, Vince
S. Buffalo

In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis.  biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.