pxrr(1)

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>