NAME¶

pxrr - reroot (or unroot) a tree file and produce a newick

SYNOPSIS¶

pxrr [OPTIONS]...

DESCRIPTION¶

Reroot (or unroot) a tree file and produce a newick. 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 tree file, STDIN otherwise

-g, --outgroups=CSL

outgroup sep by commas (NO SPACES!)

-f, --namesf=FILE

outgroups in a file (each on a line)

-r, --ranked

turn on ordering of outgroups. will root on first one present

-u, --unroot

unroot the tree

-s, --silent

do not error if outgroup(s) not found

-o, --outf=FILE

output tree 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 Stephen A. Smith (blackrim), Joseph W. Brown

REPORTING BUGS¶

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

COPYRIGHT¶

Copyright © 2014-2021 FePhyFoFum License GPLv3