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