write.pml: Export pml objects

In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis

Export pml objects

Description

write.pml writes out the ML tree and the model parameters.

Usage

write.pml(x, file = "pml", save_rds = TRUE, ...)

Arguments

x	an object of class ancestral.
file	a file name. File endings are added.
save_rds	logical, if TRUE saves the pml object as a rds file, otherwise the alignment is saved as a fasta file.
...	Further arguments passed to or from other methods.

Value

write.pml returns the input x invisibly.

See Also

ancestral.pml, plotAnc

Examples

data(woodmouse)
fit <- pml_bb(woodmouse, "JC", rearrangement = "none")
write.pml(fit, "woodmouse")
unlink(c("woodmouse_pml.txt", "woodmouse_tree.nwk", "woodmouse.rds"))

KlausVigo/phangorn documentation built on Nov. 20, 2024, 12:47 p.m.