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

Author

       Written by Stephen A. Smith (blackrim), Joseph W. Brown

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.

Copyright

       Copyright © 2014-2024 FePhyFoFum License GPLv3

pxrr 1.3.1                                          June 2024                                            PXRR(1)

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.

Name

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

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

Reporting Bugs

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