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>