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]