dist_matrix: Distance matrix for multiple sequences.

In phac-nml-phrsd/angedist: Antigenic Genetic Distance

Distance matrix for multiple sequences.

Description

Distance matrix for multiple sequences.

Usage

dist_matrix(sobj, sites = NULL, ncores = 1, dist.type = "hamming")

Arguments

sobj	List of sequences object as returned by import_seqs().
sites	List of integer vectors. Positions where the differences are calculated. For example, sites = list( c(1:5), c(300:900), 1234. If sites=NULL (Default), then all sites are included in the distance calculation.
ncores	Integer. Number of cores used for parallel computation. Default ncores=1 (i.e., no parallel computation). To use all available cores, enter ncores=0.
dist.type	String. Type of genetic distance. Default dist.type='hamming'. Options are 'hamming', 'blosum'.

Value

A distance matrix.

phac-nml-phrsd/angedist documentation built on Nov. 27, 2022, 7:23 p.m.