phylo2mafft: Convert Trees for MAFFT

In ips: Interfaces to Phylogenetic Software in R

Convert Trees for MAFFT

Description

Converts a phylogenetic tree of class "phylo" to a format usable as a guide tree by MAFFT. This function is called internally by mafft.

Usage

phylo2mafft(phy, file)

Arguments

phy	A phylogenetic tree of class phylo.
file	A character string giving a filename. May be missing, in which case the results are only printed on the screen.

Value

A matrix coding the MAFFT-formatted tree, as a side effect the same matrix is written to file.

References

The MAFFT website: https://mafft.cbrc.jp/alignment/software/index.html

See Also

mafft for an interface to MAFFT.

ips documentation built on May 29, 2024, 4:39 a.m.