buildPML: Wrapper for phangorn::optim.pml

In dowser: B Cell Receptor Phylogenetics Toolkit

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,
  optEdge = TRUE,
  verbose = FALSE,
  resolve_random = TRUE,
  quiet = 0,
  rep = NULL,
  dir = NULL,
  id = NULL,
  asrp = FALSE
)

Arguments

clone	airrClone object
seq	sequence 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
optEdge	Optimize edge lengths
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)
dir	A directory to save the codon table
id	The identifier value
asrp	Get the codon table?

Value

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

dowser documentation built on Nov. 5, 2025, 6:36 p.m.