NAME¶

pxcltr - general tree cleaner

SYNOPSIS¶

pxcltr [OPTIONS]...

DESCRIPTION¶

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.

AUTHOR¶

Written by Joseph W. Brown

REPORTING BUGS¶

Report bugs to: <https://github.com/FePhyFoFum/phyx/issues> phyx home page: <https://github.com/FePhyFoFum/phyx>

COPYRIGHT¶

Copyright © 2017-2021 FePhyFoFum License GPLv3