pxaa2cdn1
Generate codon alignment from aligned amino acids and unaligned nucleotides
Usage
pxaa2cdn [OPTIONS] ...
Overview
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.
History
- Debian 13 (Trixie): the text shown here
- Debian 12 (Bookworm)
- Debian 10 (Buster)
--citation since Debian 12 (Bookworm);
--rmlastcdn since Debian 12 (Bookworm);
--stopremove since Debian 13 (Trixie);
-C since Debian 12 (Bookworm);
-r since Debian 12 (Bookworm);
-s since Debian 13 (Trixie).