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 © 2015-2021 FePhyFoFum License GPLv3