NAME

       pxaa2cdn - generate codon alignment from aligned amino acids and unaligned nucleotides

SYNOPSIS

       pxaa2cdn [OPTIONS]...

DESCRIPTION

       Generate  a  codon  alignment  from  aligned amino acids and unaligned nucleotides.  Taxa found in only 1
       input file will be removed.  This will take fasta, fastq, phylip, and nexus inputs.

OPTIONS

       -a, --aaseqf=FILE
              input sequence file, STDIN otherwise

       -n, --nucseqf=FILE
              input sequence file, STDIN otherwise

       -r, --rmlastcdn
              remove last codon from *all* nuc sequences (default: false)

       -s, --stopremove
              remove stop codon from nuc sequences if present (default: false)

       -o, --outf=FILE
              output fasta 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 F. Walker, 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 © 2015-2024 FePhyFoFum License GPLv3

pxaa2cdn 1.3.1                                      June 2024                                        PXAA2CDN(1)