NAME

       alignment-translate - Translate a DNA/RNA alignment into amino acids.

SYNOPSIS

       alignment-translate [OPTIONS] < sequence-file [OPTIONS]

DESCRIPTION

       Translate a DNA/RNA alignment into amino acids.

ALLOWED OPTIONS:

       -h, --help
              Produce help message

       -g arg (=standard), --genetic-code arg (=standard)
              Specify alternate genetic code.

       -f arg (=1), --frame arg (=1)
              Frame 1, 2, 3, -1, -2, or -3

       -r, --reverse
              Just return the reverse

       -c, --complement
              Just return the complement

       -t arg (=yes), --translate arg (=yes)
              Translate the sequences

EXAMPLES:

       Translate DNA or RNA to amino acids in reading frame 1:

              % alignment-translate < dna.fasta > aa.fasta

       Give the reverse complement without translation:

              % alignment-translate -rc --translate=no < dna.fasta > dna2.fasta

       The following commands are identical:

              % alignment-translate --frame=-2 < dna.fasta > aa2.fasta
              % alignment-translate -rc --frame=2 < dna.fasta > aa2.fasta

REPORTING BUGS:

       BAli-Phy online help: <http://www.bali-phy.org/docs.php>.

       Please send bug reports to <bali-phy-users@googlegroups.com>.

AUTHORS

       Benjamin Redelings.

                                             Feb 2018                      alignment-translate(1)