buildPratchet - 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.