parse RAxML bootstrapping analysis output
Examples
raxml_file <- system.file("extdata/RAxML", "RAxML_bipartitionsBranchLabels.H3", package="treeio")
read.raxml(raxml_file)
#> 'treedata' S4 object that stored information
#> of
#> '/usr/local/lib/R/site-library/treeio/extdata/RAxML/RAxML_bipartitionsBranchLabels.H3'.
#>
#> ...@ phylo:
#>
#> Phylogenetic tree with 64 tips and 62 internal nodes.
#>
#> Tip labels:
#> A_Hokkaido_M1_2014_H3N2_2014, A_Czech_Republic_1_2014_H3N2_2014,
#> FJ532080_A_California_09_2008_H3N2_2008,
#> EU199359_A_Pennsylvania_05_2007_H3N2_2007,
#> EU857080_A_Hong_Kong_CUHK69904_2006_H3N2_2006,
#> EU857082_A_Hong_Kong_CUHK7047_2005_H3N2_2005, ...
#>
#> Unrooted; includes branch lengths.
#>
#> with the following features available:
#> 'bootstrap'.
#>
#> # The associated data tibble abstraction: 126 × 4
#> # The 'node', 'label' and 'isTip' are from the phylo tree.
#> node label isTip bootstrap
#> <int> <chr> <lgl> <dbl>
#> 1 1 A_Hokkaido_M1_2014_H3N2_2014 TRUE NA
#> 2 2 A_Czech_Republic_1_2014_H3N2_2014 TRUE NA
#> 3 3 FJ532080_A_California_09_2008_H3N2_2008 TRUE NA
#> 4 4 EU199359_A_Pennsylvania_05_2007_H3N2_2007 TRUE NA
#> 5 5 EU857080_A_Hong_Kong_CUHK69904_2006_H3N2_2006 TRUE NA
#> 6 6 EU857082_A_Hong_Kong_CUHK7047_2005_H3N2_2005 TRUE NA
#> 7 7 YGSIV1046_Sw_Binh_Duong_03_10_2010 TRUE NA
#> 8 8 YGSIV1044_Sw_Binh_Duong_03_08_2010 TRUE NA
#> 9 9 YGSIV1522_SW_HK_1071_2012 TRUE NA
#> 10 10 YGSIV1534_SW_HK_2454_2012 TRUE NA
#> # ℹ 116 more rows