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