read HYPHY output

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 #> '/cache/treeio/extdata/HYPHY/labelledtree.tree'. #> #> [email protected] 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.