read.hyphy: read.hyphy
In treeio: Base Classes and Functions for Phylogenetic Tree Input and Output

Description Usage Arguments Value Author(s) Examples

read HYPHY output

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

`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

A hyphy object

Guangchuang Yu https://guangchuangyu.github.io

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

'hyphy' S4 object that stored information of 
	 '/usr/local/lib/R/site-library/treeio/extdata/HYPHY/labelledtree.tree'and '/usr/local/lib/R/site-library/treeio/extdata/HYPHY/ancseq.nex' .
...@ tree:
Phylogenetic tree with 15 tips and 13 internal nodes.

Tip labels:
	K, N, D, L, J, G, ...
Node labels:
	Node1, Node2, Node3, Node4, Node5, Node12, ...

Unrooted; includes branch lengths.

with the following features available:
	'tip sequence not available...
'.
Warning message:
In get.fields(object) : tip sequence not available...