expand.distance.matrix: Updates a pre-existing distance matrix

In Hackout3/saphy: Sequential Analysis of Phylogenies

Description

expand.distance.matrix updates a pairwise distance matrix with distances calculated between the existing alignment and an additional sequence (assumed to be aligned)

Usage

expand.distance.matrix(aln, s, distmat = NULL, model = "TN93",
  gamma = FALSE)

Arguments

aln	a multiple sequence alignment
s	a nucleotide sequence
distmat	a distance matrix (as a standard matrix). If NULL, then a distance matrix is computed.
model	a model of nucleotide substitution (default=TN93)
gamma	the gamma parameter of rate variation

Value

A list with two elements: distmat, a distance matrix (as a standard R matrix), and aln, an updated alignment.

Author(s)

Simon Frost ([e-mail])

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