taxdumpSubset: Utilities for NCBI Taxdump

In heibl/megaptera: MEGAPhylogeny Techniques in R

Description

Get subset of a taxonomy table in parent-child format.

Usage

taxdumpSubset(tax, mrca, species, root = "tol", syn = FALSE)

Arguments

tax	Either an object of class megapteraProj or a data frame containing a taxonomy table in parent-child format as returned by dbReadTaxonomy.
mrca	A character string giving the most recent common ancestor (MRCA) of the subset.
species	A vector of mode "character" giving a subset of species names.
root	A character string choosing between "mrca" and "tol" (tree of life).
syn	Logical, indicating if synonyms should be returned in addition to accepted names; only has an effect if tax is of class megapteraProj.

See Also

dbReadTaxonomy, taxdumpChildren,taxdumpLineage, taxdumpAddNode, taxdump2phylo.

heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.