read mlc file of codeml output

read.codeml_mlc(mlcfile)

Arguments

mlcfile

mlc file

Value

A codeml_mlc object

Author

Guangchuang Yu

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'.
#> 
#> [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:
#> 	'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  
#> # … with 18 more rows