tax2phylo: converts an NCBI taxonomy object to an 'ape::phylo' tree

In raim/ncbitax: Simple base R parser for NCBI Taxonomy

Description

converts an NCBI taxonomy object to an ape::phylo tree

Usage

tax2phylo(tax, root = "1", names = FALSE, order = FALSE)

Arguments

tax	NCBI taxonomy object
root	taxon ID of the taxonomic class to be considered as root
names	replace taxon IDs by names
order	order edges, required for attribute "cladewise" of the returned ape::phylo tree

Examples

phy <- tax2phylo(tax, root="1890428", order=TRUE, names=TRUE)
ape::plot.phylo(phy)

raim/ncbitax documentation built on Aug. 6, 2020, 7:29 a.m.