jplaceExpand: Expanded '.jplace' files.

In fkeck/diatobc: Bioinformatic toolbox for my projects

Description

This is an utility function to expand .jplace files generated by RAxML and pplacer.

Usage

jplaceExpand(input, output, round.brlen = 6, likw.max = NA)

Arguments

input	Input file, absolute path or relative to the current working directory (a jplace file).
output	Ouput file, absolute path or relative to the current working directory (a jplace file). If set to NULL, file content is returned in R directly as a character string.
round.brlen	numeric value. Number of digits to round branch lengths of the tree. If NA, the tree is not modified.
likw.max	numeric value. If not NA, the replacements with an inferior likelihood weight are dropped.

Details

This utility function is used to generate .jplace files which can be used with the function tog of guppy to get phylogenetic trees.

References

Matsen F.A., Hoffman N.G., Gallagher A. & Stamatakis A. (2012) A Format for Phylogenetic Placements. PLoS ONE 7, e31009.

fkeck/diatobc documentation built on May 12, 2019, 7:18 p.m.