read beast/mrbayes/mega Nexus output
read beast/mrbayes/mega newick file format
read.beast(file) read.mrbayes(file) read.beast.newick(file) read.mega(file)
Arguments
| file | newick file |
|---|
Value
treedata object
treedata object
Author
Guangchuang Yu https://guangchuangyu.github.io
Bradley R Jones
Examples
file <- system.file("extdata/BEAST", "beast_mcc.tree", package="treeio") read.beast(file) #> 'treedata' S4 object that stored information of #> '/usr/local/lib/R/site-library/treeio/extdata/BEAST/beast_mcc.tree'. #> #> [email protected] phylo: #> #> Phylogenetic tree with 15 tips and 14 internal nodes. #> #> Tip labels: #> A_1995, B_1996, C_1995, D_1987, E_1996, F_1997, ... #> #> Rooted; includes branch lengths. #> #> with the following features available: #> 'height', 'height_0.95_HPD', 'height_median', 'height_range', 'length', #> 'length_0.95_HPD', 'length_median', 'length_range', 'posterior', 'rate', #> 'rate_0.95_HPD', 'rate_median', 'rate_range'. #> #> # The associated data tibble abstraction: 29 × 16 #> # The 'node', 'label' and 'isTip' are from the phylo tree. #> node label isTip height height_0.95_HPD height_median height_range length #> <int> <chr> <lgl> <dbl> <list> <dbl> <list> <dbl> #> 1 1 A_1995 TRUE 18 <dbl [2]> 18 <dbl [2]> 1.34 #> 2 2 B_1996 TRUE 17 <dbl [2]> 17 <dbl [2]> 3.30 #> 3 3 C_1995 TRUE 18 <dbl [2]> 18 <dbl [2]> 3.33 #> 4 4 D_1987 TRUE 26 <dbl [2]> 26 <dbl [2]> 9.14 #> 5 5 E_1996 TRUE 17 <dbl [2]> 17 <dbl [2]> 3.29 #> 6 6 F_1997 TRUE 16 <dbl [2]> 16 <dbl [2]> 0.849 #> 7 7 G_1992 TRUE 21 <dbl [2]> 21 <dbl [2]> 5.21 #> 8 8 H_1992 TRUE 21 <dbl [2]> 21 <dbl [2]> 2.19 #> 9 9 I_1994 TRUE 19 <dbl [2]> 19 <dbl [2]> 1.76 #> 10 10 J_1983 TRUE 30 <dbl [2]> 30 <dbl [2]> 1.60 #> # … with 19 more rows, and 8 more variables: length_0.95_HPD <list>, #> # length_median <dbl>, length_range <list>, posterior <dbl>, rate <dbl>, #> # rate_0.95_HPD <list>, rate_median <dbl>, rate_range <list> file <- system.file("extdata/MrBayes", "Gq_nxs.tre", package="treeio") read.mrbayes(file) #> 'treedata' S4 object that stored information of #> '/usr/local/lib/R/site-library/treeio/extdata/MrBayes/Gq_nxs.tre'. #> #> [email protected] phylo: #> #> Phylogenetic tree with 12 tips and 10 internal nodes. #> #> Tip labels: #> B_h, B_s, G_d, G_k, G_q, G_s, ... #> #> Unrooted; includes branch lengths. #> #> with the following features available: #> 'length_0.95HPD', 'length_mean', 'length_median', 'prob', 'prob_range', #> 'prob_stddev', 'prob_percent', 'prob+-sd'. #> #> # The associated data tibble abstraction: 22 × 11 #> # The 'node', 'label' and 'isTip' are from the phylo tree. #> node label isTip length_0.95HPD length_mean length_median prob prob_range #> <int> <chr> <lgl> <list> <chr> <chr> <chr> <list> #> 1 1 B_h TRUE <dbl [2]> 0.1434667402… 0.1431799378… 1 <dbl [2]> #> 2 2 B_s TRUE <dbl [2]> 0.1925054374… 0.1922242167… 1 <dbl [2]> #> 3 3 G_d TRUE <dbl [2]> 0.0547261328… 0.0546279278… 1 <dbl [2]> #> 4 4 G_k TRUE <dbl [2]> 0.0628571252… 0.0627032472… 1 <dbl [2]> #> 5 5 G_q TRUE <dbl [2]> 0.0632261126… 0.0631496765… 1 <dbl [2]> #> 6 6 G_s TRUE <dbl [2]> 0.0105788053… 0.0103911008… 1 <dbl [2]> #> 7 7 G_t TRUE <dbl [2]> 0.0072686054… 0.0071387519… 1 <dbl [2]> #> 8 8 M_s TRUE <dbl [2]> 0.2950272225… 0.2943109745… 1 <dbl [2]> #> 9 9 N_m TRUE <dbl [2]> 0.2277924813… 0.2275137837… 1 <dbl [2]> #> 10 10 P_h TRUE <dbl [2]> 0.2250534499… 0.2250620826… 1 <dbl [2]> #> # … with 12 more rows, and 3 more variables: prob_stddev <chr>, #> # prob_percent <chr>, prob+-sd <chr> tree <- read.beast.newick(textConnection('(a[&rate=1]:2,(b[&rate=1.1]:1,c[&rate=0.9]:1)[&rate=1]:1);'))