read HYPHY output
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
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/lib/R/site-library/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.