mltree {orthGS} | R Documentation |
Build Up a ML Tree
Description
Given an alignment builds an ML tree.
Usage
mltree(msa, df = TRUE, gapl = TRUE, model = "WAG")
Arguments
msa |
input alignment. |
df |
logical. When TRUE msa should be a dataframe, when FALSE msa should be a string giving the path to a fasta file containing the alignment. |
gapl |
logical, when TRUE a gapless alignment is used. |
model |
allows to choose an amino acid models (see the function phangorn::as.pml) |
Details
The function makes a NJ tree and then improve it using an optimization procedure based on ML.
Value
a ML optimized tree (and parameters)
See Also
gapless_msa
Examples
## Not run: a <- msa(sequences=c("RAPGT", "KMPGT", "ESGGT"), ids = letters[1:3])$ali
rownames(a) <- letters[1:3]
tr <- mltree(a)$tree
## End(Not run)
[Package orthGS version 0.1.8 Index]