read MCMCTree output Tree
Arguments
- file
the output tree file of MCMCTree
- force.ultrametric
logical whether convert the tree to be ultrametric, if it is not ultrametric, default is FALSE. When the tree is ultrametric, branch times will be calculated automatically.
Examples
file <- system.file("extdata/MCMCTree", "mcmctree_output.tree", package="treeio")
tr <- read.mcmctree(file)
tr
#> 'treedata' S4 object that stored information
#> of
#> '/usr/local/lib/R/site-library/treeio/extdata/MCMCTree/mcmctree_output.tree'.
#>
#> ...@ phylo:
#>
#> Phylogenetic tree with 103 tips and 102 internal nodes.
#>
#> Tip labels:
#> Dioscorea_villosa, Colchicum_autumnale, Smilax_bona-nox, Sorghum_bicolor,
#> Zea_mays, Oryza_sativa, ...
#>
#> Rooted; includes branch lengths.
#>
#> with the following features available:
#> '0.95', 'reltime'.
#>
#> # The associated data tibble abstraction: 205 × 5
#> # The 'node', 'label' and 'isTip' are from the phylo tree.
#> node label isTip `0.95` reltime
#> <int> <chr> <lgl> <list> <dbl>
#> 1 1 Dioscorea_villosa TRUE <NULL> NA
#> 2 2 Colchicum_autumnale TRUE <NULL> NA
#> 3 3 Smilax_bona-nox TRUE <NULL> NA
#> 4 4 Sorghum_bicolor TRUE <NULL> NA
#> 5 5 Zea_mays TRUE <NULL> NA
#> 6 6 Oryza_sativa TRUE <NULL> NA
#> 7 7 Brachypodium_distachyon TRUE <NULL> NA
#> 8 8 Sabal_bermudana TRUE <NULL> NA
#> 9 9 Yucca_filamentosa TRUE <NULL> NA
#> 10 10 Acorus_americanus TRUE <NULL> NA
#> # ℹ 195 more rows