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
#> 	'/usr/local/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.
#> 
#>  None available features.
#> # The associated data tibble abstraction: 28 × 3
#> # The 'node', 'label' and 'isTip' are from the phylo tree.
#>     node label isTip
#>    <int> <chr> <lgl>
#>  1     1 K     TRUE 
#>  2     2 N     TRUE 
#>  3     3 D     TRUE 
#>  4     4 L     TRUE 
#>  5     5 J     TRUE 
#>  6     6 G     TRUE 
#>  7     7 C     TRUE 
#>  8     8 E     TRUE 
#>  9     9 O     TRUE 
#> 10    10 H     TRUE 
#> # … with 18 more rows