read.hyphy {treeio} | R Documentation

## read.hyphy

### Description

read HYPHY output

### Usage

    read.hyphy(nwk, ancseq, tip.fasfile = NULL)

### Arguments

`nwk` | tree file in nwk format, one of hyphy output
`ancseq` | ancestral sequence file in nexus format, one of hyphy output
`tip.fasfile` | tip sequence file

### Value

A hyphy object

### Author(s)

Guangchuang Yu https://guangchuangyu.github.io

### Examples

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

[Package treeio version 1.6.2 Index]