Build a phylogenetic tree by neighbor-joining or maximum parsimony

Builds a tree from a DNA alignment and its SNP distance matrix. A neighbor-joining tree is computed first and rooted on the most divergent isolate (the one with the largest mean SNP distance); with method = "pars" this is then refined into a maximum-parsimony tree.

Usage

get_phylo_tree(dna_aln, snp_dist, method = c("nj", "pars"))

Arguments

dna_aln

A DNA alignment object of class DNAbin.

snp_dist

A numeric matrix of SNP distances between sequences. See get_snp_dist_matrix().

method

Tree-construction method: "nj" (neighbor-joining) or "pars" (maximum parsimony).

Value

An object of class phylo representing the phylogenetic tree.