buildRAxML {dowser}

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,
  ...
)

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)

Value

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