.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH PXAA2CDN "1" "May 2018" "pxaa2cdn 0.99+ds" "User Commands"
.SH NAME
pxaa2cdn \- Takes in AA alignment and unaligned Nucleotide file to give a Codon Alignment.
.SH SYNOPSIS
.B pxaa2cdn
[\fI\,OPTION\/\fR]...
.SH DESCRIPTION
Takes in AA alignment and unaligned Nucleotide file to give a Codon Alignment.
This will get rid of any sequences found in either only the Nucleotide or the Amino Acid Alignment
This will take fasta, fastq, phylip, and nexus inputs.
.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\-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
.SH "REPORTING BUGS"
Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
phyx home page: <https://github.com/FePhyFoFum/phyx>
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.