pxcltr1

Usage

Overview

General tree cleaner. Removes annotations (node labels), 'knuckles' (2-degree nodes), and root edges to generate a 'vanilla' newick representation. By default removes all properties. Alternatively choose 1 property. This will take a newick- or nexus-formatted tree from a file or STDIN. Output is written in newick format.

Options

-t, --treef=FILE

input treefile, STDIN otherwise

-r, --root

remove root edge (if present)

-l, --labels

remove internal node labels

-k, --knuckles

remove 2-degree internal nodes

-o, --outf=FILE

output file, STOUT otherwise

-h, --help

display this help and exit

-V, --version

display version and exit

-C, --citation

display phyx citation and exit

Citation

Brown, Joseph W., Joseph F. Walker, and Stephen A. Smith. 2017. Phyx: phylogenetic tools for unix. Bioinformatics 33(12): 1886-1888. https://doi.org/10.1093/bioinformatics/btx063.