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.TH "alignment-translate" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignment-translate\f[R] - Translate a DNA/RNA alignment into amino
acids.
.SH SYNOPSIS
.PP
\f[B]alignment-translate\f[R] [OPTIONS] < sequence-file [OPTIONS]
.SH DESCRIPTION
.PP
Translate a DNA/RNA alignment into amino acids.
.SH ALLOWED OPTIONS:
.TP
\f[B]-h\f[R], \f[B]--help\f[R]
Produce help message
.TP
\f[B]-g\f[R] \f[I]arg\f[R] (=standard), \f[B]--genetic-code\f[R] \f[I]arg\f[R] (=standard)
Specify alternate genetic code.
.TP
\f[B]-f\f[R] \f[I]arg\f[R] (=1), \f[B]--frame\f[R] \f[I]arg\f[R] (=1)
Frame 1, 2, 3, -1, -2, or -3
.TP
\f[B]-r\f[R], \f[B]--reverse\f[R]
Just return the reverse
.TP
\f[B]-c\f[R], \f[B]--complement\f[R]
Just return the complement
.TP
\f[B]-t\f[R] \f[I]arg\f[R] (=yes), \f[B]--translate\f[R] \f[I]arg\f[R] (=yes)
Translate the sequences
.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[R]
.fi
.PP
Give the reverse complement without translation:
.IP
.nf
\f[C]
% alignment-translate -rc --translate=no < dna.fasta > dna2.fasta
\f[R]
.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[R]
.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.