buildPratchet - Wrapper for phangorn::pratchet
Wrapper for phangorn::pratchet
buildPratchet( clone, seq = "sequence", asr = "seq", asr_thresh = 0.05, tree = NULL, asr_type = "MPR", verbose = 0, resolve_random = TRUE, data_type = "DNA" )
- sequece column in
- return sequence or probability matrix?
- threshold for including a nucleotide as an alternative
- fixed tree topology if desired.
- MPR or ACCTRAN
- amount of rubbish to print
- randomly resolve polytomies?
- Are sequences DNA or AA?
phylo object created by phangorn::pratchet with nodes
attribute containing reconstructed sequences.