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 © 2018-2024 FePhyFoFum License GPLv3

pxrlt 1.3.1                                         June 2024                                           PXRLT(1)