.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH PXTLATE "1" "July 2021" "pxtlate 1.3" "User Commands"
.SH NAME
pxtlate \- manual page for pxtlate 1.3
.SH SYNOPSIS
.B pxtlate
[\fI\,OPTIONS\/\fR]...
.SH DESCRIPTION
Translate DNA alignment to amino acids.
This will take fasta, fastq, phylip, and nexus formats from a file or STDIN.
NOTE: assumes sequences are in frame.
.SH OPTIONS
.TP
\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
input nucleotide sequence file, STDIN otherwise
.TP
\fB\-t\fR, \fB\-\-table\fR=\fI\,STRING\/\fR
which translation table to use. currently available:
\&'std' (standard, default)
\&'vmt' (vertebrate mtDNA)
\&'ivmt' (invertebrate mtDNA)
\&'ymt' (yeast mtDNA)
.TP
\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
output aa sequence 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