tax2phylo

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

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