woodmouse

This is a set of 15 sequences of the mitochondrial gene cytochrome
 b of the woodmouse (Apodemus sylvaticus) which is a
 subset of the data analysed by Michaux et al. (2003). The full data
 set is available through GenBank (accession numbers AJ511877 to
 AJ511987).

datasets

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 DNA sequences, 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, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. 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, MAFFT) whose results are returned into R.

Emmanuel Paradis

Analyses of Phylogenetics and Evolution

woodmouse function

An object of class <code>"DNAbin"</code>.

Format

Michaux, J. R., Magnanou, E., Paradis, E., Nieberding, C. and Libois,
 R. (2003) Mitochondrial phylogeography of the Woodmouse
 (Apodemus sylvaticus) in the Western Palearctic region.
 Molecular Ecology, 12, 685--697.

woodmouse: Cytochrome b Gene Sequences of Woodmice

Description

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See Also

Examples