read mlc file of codeml output
Examples
mlcfile <- system.file("extdata/PAML_Codeml", "mlc", package="treeio")
read.codeml_mlc(mlcfile)
#> 'treedata' S4 object that stored information
#> of
#> '/usr/local/lib/R/site-library/treeio/extdata/PAML_Codeml/mlc'.
#>
#> ...@ 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:
#> 't', 'N', 'S', 'dN_vs_dS', 'dN', 'dS', 'N_x_dN', 'S_x_dS'.
#>
#> # The associated data tibble abstraction: 28 × 11
#> # The 'node', 'label' and 'isTip' are from the phylo tree.
#> node label isTip t N S dN_vs_dS dN dS N_x_dN S_x_dS
#> <dbl> <chr> <lgl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 A TRUE 0.01 1515. 633. 0.0646 0.0007 0.0101 1 6.4
#> 2 2 B TRUE 0.032 1515. 633. 0.0001 0 0.0358 0 22.7
#> 3 3 C TRUE 0.028 1515. 633. 0.0461 0.0013 0.0282 2 17.9
#> 4 4 D TRUE 0.082 1515. 633. 0.0385 0.0033 0.0849 5 53.8
#> 5 5 E TRUE 0.031 1515. 633. 0.0641 0.002 0.0305 3 19.3
#> 6 6 F TRUE 0.007 1515. 633. 0.298 0.0013 0.0044 2 2.8
#> 7 7 G TRUE 0.046 1515. 633. 0.162 0.006 0.0373 9.2 23.6
#> 8 8 H TRUE 0.021 1515. 633. 0.103 0.002 0.0191 3 12.1
#> 9 9 I TRUE 0.015 1515. 633. 0.0001 0 0.0167 0 10.6
#> 10 10 J TRUE 0.014 1515. 633. 0.0457 0.0007 0.0143 1 9
#> # ℹ 18 more rows