I have the impression that alignment-free algorithms might be for people who don't believe in evolution lol, so they cannot use it because that would (indirectly) contradict their dogma. For all others, I think they could use the algorithm with best performance.
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Michael Dondrup
I too am looking out for such a program. Not for COG finding though. Did someone try to cluster protein sequences using compositional features ?
re Leena In short yes. See i.e. the paper http://www.pnas.org/content/105/40/15352.short
What's a COG category? Can you elaborate on the problem?
It's unlikely such a program could exist. Something as simple as amino acid composition would not be able to accurately discriminate millions of proteins into a few thousand categories.
It's an old question, so you are possibly not looking anymore, but why would you need an alignment free algorithm?