Runs the whole analysis

Usage

BatchRun(taxon, mintaxa = 10, ncbi_path = "/usr/local/bin", raxml = "raxmlHPC")

Arguments

taxon

A clade in NCBI taxonomy

mintaxa

How many taxa are needed for a gene to be included

ncbi_path

Path to where NCBI tools are installed

raxml

Name of raxml executable; include full path if not in $PATH

This starts the analysis; if you already started and the computer crashed, this will pick it up from where it left off. It will run in the current working directory.

The clade in NCBI should map to a single NCBI id; if you have a synonym, try specifying search terms for rentrez::entrez_search so that it finds the correct id.

Value

Nothing, though see the directory of output