buildPML - Wrapper for phangorn::optim.pml
Wrapper for phangorn::optim.pml
buildPML( clone, seq = "sequence", sub_model = "GTR", gamma = FALSE, asr = "seq", asr_thresh = 0.05, tree = NULL, data_type = "DNA", optNni = TRUE, optQ = TRUE, verbose = FALSE, resolve_random = TRUE, quiet = 0, rep = NULL )
- sequece column in
- substitution model to use
- gamma site rate variation?
- return sequence or probability matrix?
- threshold for including a nucleotide as an alternative
- fixed tree topology if desired.
- Are sequences DNA or AA?
- Optimize tree topology
- Optimize Q matrix
- Print error messages as they happen?
- randomly resolve polytomies?
- amount of rubbish to print to console
- current bootstrap replicate (experimental)
phylo object created by phangorn::optim.pml with nodes
attribute containing reconstructed sequences.