Man page - pxaa2cdn(1)

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Package: phyx
apt-get install phyx

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phyx

Manual

PXAA2CDN

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
CITATION
AUTHOR
REPORTING BUGS
COPYRIGHT

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>