Scroll to navigation

alignment-translate(1) 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:

Produce help message
Specify alternate genetic code.
Frame 1, 2, 3, -1, -2, or -3
Just return the reverse
Just return the complement
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