mat3


  Three matrices respectively representing Serological (asymmetric),
  DNA hybridization (asymmetric) and Anatomical (symmetric) distances
  among 9 families.


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

mat3 function

A data frame with 27 observations and 9 variables.

Format

Lapointe, F.-J., J. A. W. Kirsch and J. M. Hutcheon. 1999. Total
  evidence, consensus, and bat phylogeny: a distance-based
  approach. Molecular Phylogenetics and Evolution 11: 55-66.

mat3: Three Matrices

Description

Usage

Arguments

Format

Source

See Also