comprehensiveGuidetree: Comprehensive Guide Tree

In heibl/megaptera: MEGAPhylogeny Techniques in R

Description

Creates a complete (or comprehensive) guide tree for the alignment of sequences based on the underlying taxonomic classification. If available (see taxonGuidetree), a user-defined guide tree of higher ranks will be incorporated to enhance the resolution of the comprehensive guide tree.

Usage

comprehensiveGuidetree(megProj, tip.rank, subset)

Arguments

megProj	An object of class megapteraProj.
tip.rank	A character string giving the rank of the tips (e.g. species, genus, ...).
subset	A subset of species names the taxonomy should be limited to. This can be a DNA alignment of class DNAbin, a phylogenetic tree of class phylo, a data frame or a character vector listing the species names.

Details

It can be desirable to include a user-defined guide tree for two reasons. First, one might favor another phylogenetic hypothesis than inherent in the NCBI classification. Second, no classification can provide intra-rank phylogenetic relationships, but an explicit phylogeny does. Hence, via the user-defined guide tree, it is possible to add more resolution to the guide tree topology.

Value

An object of class phylo.

See Also

dbReadTaxonomy for reading a taxonomic classification from the postgreSQL database.

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