buildRAxML: Wrapper to build RAxML-ng trees and infer intermediate nodes

Description

Wrapper to build RAxML-ng trees and infer intermediate nodes

Usage

buildRAxML(
  clone,
  seq = "sequence",
  exec,
  model = "GTR",
  partition = NULL,
  rseed = 28,
  name = "run",
  starting_tree = NULL,
  from_getTrees = FALSE,
  rm_files = TRUE,
  asr = TRUE,
  rep = 1,
  dir = NULL,
  ...
)

Value

phylo object created by RAxML-ng with nodes attribute containing reconstructed sequences.

Arguments

clone: list of airrClone objects
seq: the phylo_seq option does this clone uses. Possible options are "sequence", "hlsequence", or "lsequence"
exec: RAxML-ng executable
model: The DNA model to be used. GTR is the default.
partition: A parameter that determines how branches are reported when partitioning. Options include NULL (default), scaled, unlinked, and linked
rseed: The random seed used for the parsimony inferences. This allows you to reproduce your results.
name: specifies the name of the output file
starting_tree: specifies a user starting tree file name and path in Newick format
from_getTrees: A logical that indicates if the desired starting tree is from getTrees and not a newick file
rm_files: remove temporary files?
asr: computes the marginal ancestral states of a tree
rep: Which repetition of the tree building is currently being run. Mainly for getBootstraps.
dir: Where the output files are to be made.
...: Additional arguments (not currently used)