.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH PXAA2CDN "1" "July 2021" "pxaa2cdn 1.3" "User Commands"
.SH NAME
pxaa2cdn \- manual page for pxaa2cdn 1.3
.SH SYNOPSIS
.B pxaa2cdn
[\fI\,OPTIONS\/\fR]...
.SH 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.
.SH OPTIONS
.TP
\fB\-a\fR, \fB\-\-aaseqf\fR=\fI\,FILE\/\fR
input sequence file, STDIN otherwise
.TP
\fB\-n\fR, \fB\-\-nucseqf\fR=\fI\,FILE\/\fR
input sequence file, STDIN otherwise
.TP
\fB\-r\fR, \fB\-\-rmlastcdn\fR
remove last codon (default: false)
.TP
\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
output fasta file, STOUT otherwise
.TP
\fB\-h\fR, \fB\-\-help\fR
display this help and exit
.TP
\fB\-V\fR, \fB\-\-version\fR
display version and exit
.TP
\fB\-C\fR, \fB\-\-citation\fR
display phyx citation and exit
.SH 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.
.SH AUTHOR
Written by Joseph F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim)
.SH "REPORTING BUGS"
Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
phyx home page: <https://github.com/FePhyFoFum/phyx>
.SH COPYRIGHT
Copyright \(co 2015\-2021 FePhyFoFum
License GPLv3