pxrls - taxon relabelling from alignments

Author

       Written by Joseph W. Brown, Stephen A. Smith (blackrim)

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 © 2016-2024 FePhyFoFum License GPLv3

pxrls 1.3.1                                         June 2024                                           PXRLS(1)

Description

       Taxon  relabelling for alignments.  This will take fasta, phylip, and nexus formats from a file or STDIN.
       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.  Results are written in fasta format.

Name

       pxrls - taxon relabelling from alignments

Options

-s, --seqf=FILE
              input seq 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

Reporting Bugs

       Report      bugs      to:      <https://github.com/FePhyFoFum/phyx/issues>      phyx      home      page:
       <https://github.com/FePhyFoFum/phyx>