table of contents
PXMONO(1) | User Commands | PXMONO(1) |
NAME¶
pxmono - monophyly checker
SYNOPSIS¶
pxmono [OPTIONS]...
DESCRIPTION¶
Monophyly checker. This will take a newick- or nexus-formatted tree from a file or STDIN.
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
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 Joseph W. Brown
REPORTING BUGS¶
Report bugs to: <https://github.com/FePhyFoFum/phyx/issues> phyx home page: <https://github.com/FePhyFoFum/phyx>
COPYRIGHT¶
Copyright © 2019-2021 FePhyFoFum License GPLv3
July 2023 | pxmono 1.3 |