read.hyphy

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

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)
#> 'treedata' S4 object that stored information
#> of
#> 	'/usr/local/lib/R/site-library/treeio/extdata/HYPHY/labelledtree.tree'.
#> 
#> ...@ phylo:
#> 
#> 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.