buildRAxML - Wrapper to build RAxML-ng trees and infer intermediate nodes
Wrapper to build RAxML-ng trees and infer intermediate nodes
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, ... )
- list of
- the phylo_seq option does this clone uses. Possible options are “sequence”, “hlsequence”, or “lsequence”
- RAxML-ng executable
- The DNA model to be used. GTR is the default.
- A parameter that determines how branches are reported when partitioning. Options include NULL (default), scaled, unlinked, and linked
- The random seed used for the parsimony inferences. This allows you to reproduce your results.
- specifies the name of the output file
- specifies a user starting tree file name and path in Newick format
- A logical that indicates if the desired starting tree is from getTrees and not a newick file
- remove temporary files?
- computes the marginal ancestral states of a tree
- Which repetition of the tree building is currently being run. Mainly for getBootstraps.
- Where the output files are to be made.
- Additional arguments (not currently used)
phylo object created by RAxML-ng with nodes attribute
containing reconstructed sequences.