pxrr1
Reroot (or unroot) a tree file and produce a newick
Usage
pxrr [OPTIONS] ...
Overview
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.
Releases
3 releases since Debian 10 (Buster); the text changed 2 times.
--citation since Debian 12 (Bookworm);
--namesf since Debian 12 (Bookworm);
--ranked since Debian 12 (Bookworm);
-C since Debian 12 (Bookworm);
-f since Debian 12 (Bookworm);
-r since Debian 12 (Bookworm).