Map taxa to open tree of life

Map taxa to open tree of life

map_to_ott(
  x,
  db,
  from = "ncbi",
  resolve_synonyms = TRUE,
  dir = NULL,
  filter_unplaced = TRUE,
  remove_na = FALSE,
  quiet = FALSE
)

Arguments

x

a DNAbin

db

an OTT taxonomic database

from

the existing taxonomic ID format

resolve_synonyms

Whether to resolve synonyms

dir

A directory containing the OTT taxonomy, required if resolve synonyms is true

filter_unplaced

Whether to filter 'bad' entries. These include incertae_sedis major_rank_conflict unplaced environmental inconsistent extinct hidden hybrid not_otu viral barren See: https://github.com/OpenTreeOfLife/reference-taxonomy/blob/master/doc/taxon-flags.md for more info

remove_na

Whether taxa that could not be mapped to the open tree of life should be removed

quiet

Whether progress should be printed to console