compute.distance.matrix: Computes a pairwise distance matrix

In Hackout3/saphy: Sequential Analysis of Phylogenies

Description

compute.distance.matrix calculates a pairwise distance matrix based on a multiple sequence alignment. It is basically a thin wrapper to dist.dna in ape, with the default model being TN93 rather than K80 and pairwise deletions considered, which returns a matrix (rather than either a dist object or a matrix).

Usage

compute.distance.matrix(aln, model = "TN93", gamma = FALSE)

Arguments

aln	a multiple sequence alignment
model	a model of nucleotide substitution (default=TN93)
gamma	the gamma parameter of rate variation

Value

A distance matrix (as a standard R matrix)

Author(s)

Simon Frost ([e-mail])

Hackout3/saphy documentation built on May 6, 2019, 10:52 p.m.