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

Description Usage Arguments Value Author(s)

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

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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 ([email protected])


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