.\" Automatically generated by Pandoc 2.2.1
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.TH "alignment\-translate" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignment\-translate\f[] \- Translate a DNA/RNA alignment into
amino acids.
.SH SYNOPSIS
.PP
\f[B]alignment\-translate\f[] [OPTIONS] < sequence\-file [OPTIONS]
.SH DESCRIPTION
.PP
Translate a DNA/RNA alignment into amino acids.
.SH ALLOWED OPTIONS:
.TP
.B \f[B]\-h\f[], \f[B]\-\-help\f[]
Produce help message
.RS
.RE
.TP
.B \f[B]\-g\f[] \f[I]arg\f[] (=standard), \f[B]\-\-genetic\-code\f[] \f[I]arg\f[] (=standard)
Specify alternate genetic code.
.RS
.RE
.TP
.B \f[B]\-f\f[] \f[I]arg\f[] (=1), \f[B]\-\-frame\f[] \f[I]arg\f[] (=1)
Frame 1, 2, 3, \-1, \-2, or \-3
.RS
.RE
.TP
.B \f[B]\-r\f[], \f[B]\-\-reverse\f[]
Just return the reverse
.RS
.RE
.TP
.B \f[B]\-c\f[], \f[B]\-\-complement\f[]
Just return the complement
.RS
.RE
.TP
.B \f[B]\-t\f[] \f[I]arg\f[] (=yes), \f[B]\-\-translate\f[] \f[I]arg\f[] (=yes)
Translate the sequences
.RS
.RE
.SH EXAMPLES:
.PP
Translate DNA or RNA to amino acids in reading frame 1:
.IP
.nf
\f[C]
%\ alignment\-translate\ <\ dna.fasta\ >\ aa.fasta
\f[]
.fi
.PP
Give the reverse complement without translation:
.IP
.nf
\f[C]
%\ alignment\-translate\ \-rc\ \-\-translate=no\ <\ dna.fasta\ >\ dna2.fasta
\f[]
.fi
.PP
The following commands are identical:
.IP
.nf
\f[C]
%\ alignment\-translate\ \-\-frame=\-2\ <\ dna.fasta\ >\ aa2.fasta
%\ alignment\-translate\ \-rc\ \-\-frame=2\ <\ dna.fasta\ >\ aa2.fasta
\f[]
.fi
.SH REPORTING BUGS:
.PP
BAli\-Phy online help: <http://www.bali-phy.org/docs.php>.
.PP
Please send bug reports to <bali-phy-users@googlegroups.com>.
.SH AUTHORS
Benjamin Redelings.