get.tree {treeio}R Documentation

get.tree method

Description

get.tree method

Usage

get.tree(object, ...)

get.tree(object, ...)

## S4 method for signature 'codeml'
get.tree(object, by = "rst", ...)

## S4 method for signature 'jplace'
get.tree(object)

## S4 method for signature 'phylip'
get.tree(object, ...)

## S4 method for signature 'phylo'
get.tree(object, ...)

## S4 method for signature 'treedata'
get.tree(object, ...)

## S4 method for signature 'hyphy'
get.tree(object)

## S4 method for signature 'paml_rst'
get.tree(object)

## S4 method for signature 'phangorn'
get.tree(object, ...)

## S4 method for signature 'codeml_mlc'
get.tree(object, ...)

## S4 method for signature 'r8s'
get.tree(object, ...)

Arguments

object

one of phylo, jplace, nhx, phangorn, beast, hyphy, codeml, codeml_mlc, paml_rst object

...

additional parameter

by

one of rst or mlc

Value

phylo object

Author(s)

Guangchuang Yu http://guangchuangyu.github.io

Examples

nwk <- system.file("extdata/HYPHY", "labelledtree.tree", package="treeio")
ancseq <- system.file("extdata/HYPHY", "ancseq.nex", package="treeio")
hy <- read.hyphy(nwk, ancseq)
get.tree(hy)

[Package treeio version 1.2.2 Index]