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