buildPML {dowser}

Wrapper for phangorn::optim.pml

Description

Wrapper for phangorn::optim.pml

Usage

buildPML(
  clone,
  seq = "sequence",
  sub_model = "GTR",
  gamma = FALSE,
  asr = "seq",
  asr_thresh = 0.05,
  tree = NULL,
  data_type = "DNA",
  optNni = TRUE,
  optQ = TRUE,
  verbose = FALSE,
  resolve_random = TRUE,
  quiet = 0,
  rep = NULL
)

Arguments

clone

airrClone object

seq

sequece column in airrClone object

sub_model

substitution model to use

gamma

gamma site rate variation?

asr

return sequence or probability matrix?

asr_thresh

threshold for including a nucleotide as an alternative

tree

fixed tree topology if desired.

data_type

Are sequences DNA or AA?

optNni

Optimize tree topology

optQ

Optimize Q matrix

verbose

Print error messages as they happen?

resolve_random

randomly resolve polytomies?

quiet

amount of rubbish to print to console

rep

current bootstrap replicate (experimental)

Value

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