table of contents
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:¶
- -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 |