tax2phylo: tax2phylo

In alexpiper/taxreturn: An R package for retrieving and curating public DNA barcode reference data

tax2phylo

Description

A newer, faster tax2tree that grafts tips. Only returns a phylo objec

Usage

tax2phylo(
  x,
  ranks = c("kingdom", "phylum", "class", "order", "family", "genus", "species"),
  depth = "all",
  summarise = FALSE,
  append_sum = TRUE,
  hex = FALSE,
  resolve_poly = FALSE
)

Arguments

x	a DNAbin object or an object coercible to DNAbin
ranks	The taxonomic ranks currently assigned to the names
depth	The depth within the ranks to return. Default all to return lowest input rank
summarise	Summarise the number of sequences at depth.
append_sum	Append the summary number to the output trees tip labels when summarise is TRUE
hex	Convert the accessions to hexadecimal format to avoid newick incompatible characters. Can be reversed with hex2acc
resolve_poly	Randomly resolve polytomies in tree using ape::multi2di. use 'all' to resolve all polytomies, or 'upper' to only resolve upper branches, useful for making constraints trees

alexpiper/taxreturn documentation built on Sept. 14, 2024, 7:56 p.m.