read.raxml: read.raxml

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

Description

parse RAxML bootstrapping analysis output

Usage

read.raxml(file)

Arguments

file	RAxML bootstrapping analysis output

Value

treedata object

Author(s)

Guangchuang Yu

Examples

raxml_file <- system.file("extdata/RAxML", "RAxML_bipartitionsBranchLabels.H3", package="treeio")
read.raxml(raxml_file)

Example output

'treedata' S4 object that stored information of
	 '/usr/local/lib/R/site-library/treeio/extdata/RAxML/RAxML_bipartitionsBranchLabels.H3'.

...@ tree: 
Phylogenetic tree with 64 tips and 62 internal nodes.

Tip labels:
	A_Hokkaido_M1_2014_H3N2_2014, A_Czech_Republic_1_2014_H3N2_2014, FJ532080_A_California_09_2008_H3N2_2008, EU199359_A_Pennsylvania_05_2007_H3N2_2007, EU857080_A_Hong_Kong_CUHK69904_2006_H3N2_2006, EU857082_A_Hong_Kong_CUHK7047_2005_H3N2_2005, ...

Unrooted; includes branch lengths.

with the following features available:
	'bootstrap'.

treeio documentation built on Nov. 21, 2020, 2:01 a.m.