read rst file from paml (both baseml and codeml) output
Author
Guangchuang Yu https://guangchuangyu.github.io
Examples
rstfile <- system.file("extdata/PAML_Baseml", "rst", package="treeio")
read.paml_rst(rstfile)
#> 'treedata' S4 object that stored information
#> of
#> '/usr/local/lib/R/site-library/treeio/extdata/PAML_Baseml/rst'.
#>
#> ...@ 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'.
#>
#> # The associated data tibble abstraction: 28 × 5
#> # The 'node', 'label' and 'isTip' are from the phylo tree.
#> node label isTip subs AA_subs
#> <dbl> <chr> <lgl> <chr> <chr>
#> 1 1 A TRUE C214T / G294T / G785A / T966C / C1641T / A1808G / … "R262K…
#> 2 2 B TRUE C222T / G555A / C732A / G785A / C828T / G939T / T9… "R262K"
#> 3 3 C TRUE A204G / C222T / G504A / A815G / C891T / G1023T / T… "N272S…
#> 4 4 D TRUE A111G / A168G / T211C / A213G / T214C / G243A / A3… "K104R…
#> 5 5 E TRUE C174T / G243A / G321A / A622T / T831C / A894G / G9… "T208S…
#> 6 6 F TRUE T829C / C1353T / A1443G / T1548C / C1645A "S277P…
#> 7 7 G TRUE A5T / A69G / G106T / C156T / C237T / G295A / G301C… "E2V /…
#> 8 8 H TRUE A112G / C132A / G774T / A792C / T1002C / G1020A / … "I38V …
#> 9 9 I TRUE T211C / C582T / C891T / A894G / G1083A / G1116A / … ""
#> 10 10 J TRUE G295A / A618G / A783C / C996T / G1593A / A1845G / … "G99R"
#> # ℹ 18 more rows