as.phylo.formula

 a right-side formula describing the taxonomic relationship: <code>~C1/C2/.../Cn</code>. 

 the data.frame where to look for the variables (default to environment). 

data

 further arguments to be passed from other methods.


  The function <code>as.phylo.formula</code> (short form <code>as.phylo</code>)
  builds a phylogenetic tree (an object of class <code>phylo</code>) from
  a set of nested taxonomic variables.


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.

as.phylo.formula: Conversion from Taxonomy Variables to Phylogenetic Trees

Description

Usage

Arguments

Value

Details

See Also

Examples