read beast/mrbayes/mega Nexus output
read beast/mrbayes/mega newick file format
Examples
file <- system.file("extdata/BEAST", "beast_mcc.tree", package="treeio")
read.beast(file)
#> 'treedata' S4 object that stored information
#> of
#> '/usr/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_0.9…¹ heigh…² heigh…³ length lengt…⁴ lengt…⁵
#> <int> <chr> <lgl> <dbl> <list> <dbl> <list> <dbl> <list> <dbl>
#> 1 1 A_1995 TRUE 18 <dbl [2]> 18 <dbl> 1.34 <dbl> 1.32
#> 2 2 B_1996 TRUE 17 <dbl [2]> 17 <dbl> 3.30 <dbl> 3.28
#> 3 3 C_1995 TRUE 18 <dbl [2]> 18 <dbl> 3.33 <dbl> 3.31
#> 4 4 D_1987 TRUE 26 <dbl [2]> 26 <dbl> 9.14 <dbl> 8.97
#> 5 5 E_1996 TRUE 17 <dbl [2]> 17 <dbl> 3.29 <dbl> 3.27
#> 6 6 F_1997 TRUE 16 <dbl [2]> 16 <dbl> 0.849 <dbl> 0.831
#> 7 7 G_1992 TRUE 21 <dbl [2]> 21 <dbl> 5.21 <dbl> 5.19
#> 8 8 H_1992 TRUE 21 <dbl [2]> 21 <dbl> 2.19 <dbl> 2.16
#> 9 9 I_1994 TRUE 19 <dbl [2]> 19 <dbl> 1.76 <dbl> 1.74
#> 10 10 J_1983 TRUE 30 <dbl [2]> 30 <dbl> 1.60 <dbl> 1.56
#> # … with 19 more rows, 6 more variables: length_range <list>, posterior <dbl>,
#> # rate <dbl>, rate_0.95_HPD <list>, rate_median <dbl>, rate_range <list>, and
#> # abbreviated variable names ¹height_0.95_HPD, ²height_median, ³height_range,
#> # ⁴length_0.95_HPD, ⁵length_median
file <- system.file("extdata/MrBayes", "Gq_nxs.tre", package="treeio")
read.mrbayes(file)
#> 'treedata' S4 object that stored information
#> of
#> '/usr/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_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_0.95…¹ lengt…² lengt…³ prob prob_…⁴ prob+…⁵ prob_…⁶
#> <int> <chr> <lgl> <list> <chr> <chr> <chr> <chr> <chr> <list>
#> 1 1 B_h TRUE <dbl [2]> 0.1434… 0.1431… 1 100 100+-0 <dbl>
#> 2 2 B_s TRUE <dbl [2]> 0.1925… 0.1922… 1 100 100+-0 <dbl>
#> 3 3 G_d TRUE <dbl [2]> 0.0547… 0.0546… 1 100 100+-0 <dbl>
#> 4 4 G_k TRUE <dbl [2]> 0.0628… 0.0627… 1 100 100+-0 <dbl>
#> 5 5 G_q TRUE <dbl [2]> 0.0632… 0.0631… 1 100 100+-0 <dbl>
#> 6 6 G_s TRUE <dbl [2]> 0.0105… 0.0103… 1 100 100+-0 <dbl>
#> 7 7 G_t TRUE <dbl [2]> 0.0072… 0.0071… 1 100 100+-0 <dbl>
#> 8 8 M_s TRUE <dbl [2]> 0.2950… 0.2943… 1 100 100+-0 <dbl>
#> 9 9 N_m TRUE <dbl [2]> 0.2277… 0.2275… 1 100 100+-0 <dbl>
#> 10 10 P_h TRUE <dbl [2]> 0.2250… 0.2250… 1 100 100+-0 <dbl>
#> # … with 12 more rows, 1 more variable: prob_stddev <chr>, and abbreviated
#> # variable names ¹length_0.95HPD, ²length_mean, ³length_median,
#> # ⁴prob_percent, ⁵`prob+-sd`, ⁶prob_range
tree <- read.beast.newick(textConnection('(a[&rate=1]:2,(b[&rate=1.1]:1,c[&rate=0.9]:1)[&rate=1]:1);'))