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⟩\c .
Please send bug reports to ⟨[email protected]⟩\c .
AUTHORS
Benjamin Redelings.