alignment-translate(1)

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.