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,
data_type = "DNA",
from_getTrees = FALSE,
rm_files = TRUE,
asr = TRUE,
rep = 1,
dir = NULL,
n_starts = NULL,
...
)
Arguments¶
- clone
- list of
airrCloneobjects - 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
- 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.