tRNA and tmRNA detection
Dean Laslett, an Australian specialist in stable RNAs, is the developer of the following software.
ARAGORN detects tRNA and tmRNA in nucleotide sequences. Version 1.1 is identical to version 1.0 when it comes to detection, but some features have been added and a bug has been fixed. The tmRNA detection algorithm is an development of the earlier published BRUCE algorithm. If your primary interest is in tmRNA detection you should also try BRUCE. BRUCE is slightly more selective than ARAGORN, but on the other hand it may in rare cases miss a tmRNA.
ARAGORN version 1.1 reports the primary sequence and the relative anticodon position. This is useful when submitting sequences to the public databases. The above additions are also available on the website.
ARWEN is the most recent development. It has a special focus on mitochondrial tRNAs from metazoan species.
optalign is a simple alignment optimizer.
ddGenerate produces real sequences from degenerated sequences (with non-ambiguous nucleotides).