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

In dowser: B Cell Receptor Phylogenetics Toolkit

Wrapper to build RAxML-ng trees and infer intermediate nodes

Description

Wrapper to build RAxML-ng trees and infer intermediate nodes

Usage

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

Arguments

clone	list of airrClone objects
exec	RAxML-ng executable
seq	the phylo_seq option does this clone uses. Possible options are "sequence", "hlsequence", or "lsequence"
sub_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
data_type	Specifies what format your data is in, DNA or AA
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.
n_starts	Number of max parsimony starting trees (default is 10 pars + 10 random)
...	Additional arguments (not currently used)

Value

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

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