mrca

getMRCA

a logical indicating whether to return the MRCAs among
    all tips and nodes (if <code>TRUE</code>); the default is to return only
    the MRCAs among tips.

full

a vector of mode numeric or character specifying the tips.


  <code>mrca</code> returns for each pair of tips (and nodes) its most
  recent common ancestor (MRCA).<p></p><p>  <code>getMRCA</code> returns the MRCA of two or more tips.
</p>

manip

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

mrca function


  <code>mrca</code> returns for each pair of tips (and nodes) its most
  recent common ancestor (MRCA).

  <code>getMRCA</code> returns the MRCA of two or more tips.


mrca: Find Most Recent Common Ancestors Between Pairs

Description

Usage

Arguments

Value

Details