beast-parser: read.beast

In GuangchuangYu/treeio: Base Classes and Functions for Phylogenetic Tree Input and Output

read.beast

Description

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)

Arguments

file	newick file
threads	number of threads for multithreading (default: 1)
verbose	set TRUE to log progress (default: FALSE)

Value

treedata object

treedata object

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

Bradley R Jones

Examples

file <- system.file("extdata/BEAST", "beast_mcc.tree", package="treeio")
read.beast(file)
file <- system.file("extdata/MrBayes", "Gq_nxs.tre", package="treeio")
read.mrbayes(file)
tr <- read.beast.newick(
        textConnection(
          '(a[&rate=1]:2,(b[&rate=1.1]:1,c[&rate=0.9]:1)[&rate=1]:1);'
        )
)

GuangchuangYu/treeio documentation built on Oct. 31, 2024, 10:13 a.m.