This function organizes higher-level information for creating variants from phylogenetic tree(s) output as phylo or multiPhylo objects (both from the ape package) or NEWICK files.

vars_phylo(obj = NULL, fn = NULL)

Arguments

obj

Object containing phylogenetic tree(s). This can be (1) a single phylo object that represents all sequences in the genome or (2) a list or multiPhylo object containing a phylo object for each reference sequence. In the latter case, phylogenies will be assigned to sequences in the order provided. Defaults to NULL.

fn

One or more string(s), each of which specifies the file name of a NEWICK file containing a phylogeny. If one name is provided, that phylogeny will be used for all sequences. If more than one is provided, there must be a phylogeny for each reference genome sequence, and phylogenies will be assigned to sequences in the order provided. Defaults to NULL.

Value

A vars_phylo_info object containing information used in create_variants to create haploid variants. This class is just a wrapper around a list containing phylogenetic tree information for each reference sequence.