read baseml output
Arguments
- rstfile
rst file
- mlcfile
mlc file
- tree
one of 'mlc' or 'rst'
- type
one of 'Marginal' or 'Joint'
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
#> '/usr/lib/R/site-library/treeio/extdata/PAML_Codeml/rst',
#> '/usr/lib/R/site-library/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'.
#>
#> # The associated data tibble abstraction: 28 × 13
#> # The 'node', 'label' and 'isTip' are from the phylo tree.
#> node label isTip subs AA_subs t N S dN_vs…¹ dN dS
#> <dbl> <chr> <lgl> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 A TRUE C214T / G2… "K603R" 0.01 1515. 633. 0.0646 0.0007 0.0101
#> 2 2 B TRUE C222T / G5… "" 0.032 1515. 633. 0.0001 0 0.0358
#> 3 3 C TRUE A204G / C2… "N272S… 0.028 1515. 633. 0.0461 0.0013 0.0282
#> 4 4 D TRUE A111G / A1… "K104R… 0.082 1515. 633. 0.0385 0.0033 0.0849
#> 5 5 E TRUE C174T / G2… "T208S… 0.031 1515. 633. 0.0641 0.002 0.0305
#> 6 6 F TRUE T829C / C1… "S277P… 0.007 1515. 633. 0.298 0.0013 0.0044
#> 7 7 G TRUE A5T / A69G… "E2V /… 0.046 1515. 633. 0.162 0.006 0.0373
#> 8 8 H TRUE A112G / C1… "I38V … 0.021 1515. 633. 0.103 0.002 0.0191
#> 9 9 I TRUE T211C / C5… "" 0.015 1515. 633. 0.0001 0 0.0167
#> 10 10 J TRUE G295A / A6… "G99R" 0.014 1515. 633. 0.0457 0.0007 0.0143
#> # … with 18 more rows, 2 more variables: N_x_dN <dbl>, S_x_dS <dbl>, and
#> # abbreviated variable name ¹dN_vs_dS