pis: Number of parsimony-informative sites

In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

Description

This function returns the number of potentially-informative(parsimony-informative) sites in DNA sequence alignment

Usage

pis(x, abs = TRUE, use.ambiguities = FALSE)

Arguments

x	object of class DNAbin
abs	logical, should the absolute or the relative number number be returned
use.ambiguities	logical, currently only FALSE is implemented, which means that IUPAC ambiguity symbols will be treated as missing information (N)

Value

numeric (the number or percentage of potentially-informative nucleotide sites)

Author(s)

Christoph Heibl

See Also

homogen.base.freq

Examples

# example data:
# -------------
data(woodmouse)	

# number of potentially-informative sites:
# ----------------------------------------
pis(woodmouse, abs = TRUE)
	
# proportion of potentially-informative sites:
# --------------------------------------------
pis(woodmouse, abs = FALSE)

fmichonneau/phyloch documentation built on May 16, 2019, 1:45 p.m.