buildPratchet {dowser}

Wrapper for phangorn::pratchet

Description

Wrapper for phangorn::pratchet

Usage

buildPratchet(
  clone,
  seq = "sequence",
  asr = "seq",
  asr_thresh = 0.05,
  tree = NULL,
  asr_type = "MPR",
  verbose = 0,
  resolve_random = TRUE,
  data_type = "DNA"
)

Arguments

clone

airrClone object

seq

sequece column in airrClone object

asr

return sequence or probability matrix?

asr_thresh

threshold for including a nucleotide as an alternative

tree

fixed tree topology if desired.

asr_type

MPR or ACCTRAN

verbose

amount of rubbish to print

resolve_random

randomly resolve polytomies?

data_type

Are sequences DNA or AA?

Value

phylo object created by phangorn::pratchet with nodes attribute containing reconstructed sequences.