read rst file from paml (both baseml and codeml) output
one of 'Marginal' or 'Joint'
Guangchuang Yu https://guangchuangyu.github.io
Loading required package: Biostrings Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:treeio': mask The following object is masked from 'package:base': strsplit 'paml_rst' S4 object that stored information of '/usr/local/lib/R/site-library/treeio/extdata/PAML_Baseml/rst'. ...@ tree: 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: 'marginal_subs', 'joint_subs', 'marginal_AA_subs', 'joint_AA_subs'.
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