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