read baseml output

read.codeml(rstfile, mlcfile, tree = "mlc", type = "Joint")

Arguments

rstfile

rst file

mlcfile

mlc file

tree

one of 'mlc' or 'rst'

type

one of 'Marginal' or 'Joint'

Value

A treedata object

Author

Guangchuang Yu

Examples

rstfile <- system.file("extdata/PAML_Codeml", "rst", package="treeio") mlcfile <- system.file("extdata/PAML_Codeml", "mlc", package="treeio") read.codeml(rstfile, mlcfile)
#> 'treedata' S4 object that stored information of #> '/cache/treeio/extdata/PAML_Codeml/rst', #> '/cache/treeio/extdata/PAML_Codeml/mlc'. #> #> [email protected] phylo: #> Phylogenetic tree with 15 tips and 13 internal nodes. #> #> Tip labels: #> A, B, C, D, E, F, ... #> Node labels: #> 16, 17, 18, 19, 20, 21, ... #> #> Unrooted; includes branch lengths. #> #> with the following features available: #> 'subs', 'AA_subs', 't', 'N', 'S', 'dN_vs_dS', 'dN', 'dS', 'N_x_dN', 'S_x_dS'.