read beast/mrbayes/mega Nexus output
read beast/mrbayes/mega newick file format
Usage
read.beast(file, threads = 1, verbose = FALSE)
read.mrbayes(file, threads = 1, verbose = FALSE)
read.beast.newick(file, threads = 1, verbose = FALSE)
read.mega(file, threads = 1, verbose = FALSE)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'.
#>
#> ...@ 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
#> # ℹ 19 more rows
#> # ℹ 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'.
#>
#> ...@ 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_percent',
#> 'prob+-sd', 'prob_range', 'prob_stddev'.
#>
#> # 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_percent
#> <int> <chr> <lgl> <list> <chr> <chr> <chr> <chr>
#> 1 1 B_h TRUE <dbl [2]> 0.14346674… 0.1431799378… 1 100
#> 2 2 B_s TRUE <dbl [2]> 0.19250543… 0.1922242167… 1 100
#> 3 3 G_d TRUE <dbl [2]> 0.05472613… 0.0546279278… 1 100
#> 4 4 G_k TRUE <dbl [2]> 0.06285712… 0.0627032472… 1 100
#> 5 5 G_q TRUE <dbl [2]> 0.06322611… 0.0631496765… 1 100
#> 6 6 G_s TRUE <dbl [2]> 0.01057880… 0.0103911008… 1 100
#> 7 7 G_t TRUE <dbl [2]> 0.00726860… 0.0071387519… 1 100
#> 8 8 M_s TRUE <dbl [2]> 0.29502722… 0.2943109745… 1 100
#> 9 9 N_m TRUE <dbl [2]> 0.22779248… 0.2275137837… 1 100
#> 10 10 P_h TRUE <dbl [2]> 0.22505344… 0.2250620826… 1 100
#> # ℹ 12 more rows
#> # ℹ 3 more variables: `prob+-sd` <chr>, prob_range <list>, prob_stddev <chr>
tr <- read.beast.newick(
textConnection(
'(a[&rate=1]:2,(b[&rate=1.1]:1,c[&rate=0.9]:1)[&rate=1]:1);'
)
)