Get phylogenetic tree using neighbor-joining or maximum parsimony method.

This function constructs a neighbor-joining or maximum parsimony phylogenetic tree from a DNA alignment object and a SNP distance matrix.

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 representing the SNP distance between sequences. See get_snp_dist_matrix() for a useful function to generate this.

method

A string indicating the method to use for tree construction. Options are "nj" (neighbor-joining) or "pars" (maximum parsimony).

Value

An object of class phylo representing the phylogenetic tree.