read_nhx {aphylo}

Read New Hampshire eXtended format for trees

Description

Read New Hampshire eXtended format for trees

Usage

read_nhx(fn, txt)

Arguments

fn

Full path to the tree file.

txt

If no file is specified, trees can also be passed as a character scalar (see examples).

Value

A list with the following elements:

• tree An object of class ape

• edge Edge annotations (length and other annotations)

• nhx A list of annotations NHX

References

"NHX - New Hampshire eXtended [version 2.0]", https://en.wikipedia.org/wiki/Newick_format#New_Hampshire_X_format

See Also

Other reading: panther-tree, read_pli()

Examples

# Example directly extracted from
# https://sites.google.com/site/cmzmasek/home/software/forester/nhx
read_nhx(
  txt = "(((ADH2:0.1[&&NHX:S=human], ADH1:0.11[&&NHX:S=human]):0.05[&&NHX:S=primates:D=Y:B=100],
    ADHY:0.1[&&NHX:S=nematode],ADHX:0.12[&&NHX:S=insect]):0.1[&&NHX:S=metazoa:D=N],
    (ADH4:0.09[&&NHX:S=yeast],ADH3:0.13[&&NHX:S=yeast], ADH2:0.12[&&NHX:S=yeast],
    ADH1:0.11[&&NHX:S=yeast]):0.1 [&&NHX:S=Fungi])[&&NHX:D=N];"
    )