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

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

       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 © 2015-2024 FePhyFoFum License GPLv3

pxaa2cdn 1.3.1                                      June 2024                                        PXAA2CDN(1)

       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.

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

-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

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

pxaa2cdn [OPTIONS]...