table of contents
PXRLT(1) | User Commands | PXRLT(1) |
NAME¶
pxrlt - taxon relabelling for trees
SYNOPSIS¶
pxrlt [OPTIONS]...
DESCRIPTION¶
Taxon relabelling for trees. Two ordered lists of taxa, -c (current) and -n (new) must be provided. Alternatively, a regex pattern (-p) and replacement (-r) text can be provided. 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
- -c, --cnames=FILE
- file containing current taxon labels (one per line)
- -n, --nnames=FILE
- file containing new taxon labels (one per line)
-p, --pattern=STRING regex pattern to replace
-r, --replace=STRING replacement pattern
- -v, --verbose
- make the output more verbose
- -o, --outf=FILE
- output 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, Stephen A. Smith (blackrim)
REPORTING BUGS¶
Report bugs to: <https://github.com/FePhyFoFum/phyx/issues> phyx home page: <https://github.com/FePhyFoFum/phyx>
COPYRIGHT¶
Copyright © 2018-2021 FePhyFoFum License GPLv3
July 2023 | pxrlt 1.3 |