buildPhylo: Wrapper for alakazam::buildPhylipLineage

In dowser: B Cell Receptor Phylogenetics Toolkit

Wrapper for alakazam::buildPhylipLineage

Description

Wrapper for alakazam::buildPhylipLineage

Usage

buildPhylo(
  clone,
  exec,
  temp_path = NULL,
  verbose = 0,
  rm_temp = TRUE,
  seq = "sequence",
  tree = NULL,
  onetree = TRUE
)

Arguments

clone	airrClone object
exec	dnapars or dnaml executable
temp_path	path to temporary directory
verbose	amount of rubbish to print
rm_temp	remove temporary files?
seq	sequece column in airrClone object
tree	fixed tree topology if desired (currently does nothing if specified)
onetree	Only sample one tree if multiple found.

Value

phylo object created by dnapars or dnaml with nodes attribute containing reconstructed sequences.

dowser documentation built on May 29, 2024, 3:06 a.m.