pxmono - monophyly checker

Author

       Written by 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 © 2019-2024 FePhyFoFum License GPLv3

pxmono 1.3.1                                        June 2024                                          PXMONO(1)

Description

       Monophyly checker.  This will take a newick- or nexus-formatted tree from a file or STDIN.

Name

       pxmono - monophyly checker

Options

-t, --treef=FILE
              input tree file, STDIN otherwise

       -n, --names=CSL
              names separated by commas (NO SPACES!)

       -f, --namesf=FILE
              names in a file (each on a line)

       -c, --comp
              take the complement (i.e. check monophyly of taxa not in list)

       -i, --ignore
              ignore missing (default: exit if names are not in the tree)

       -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>