[EMBOSS] EMBOSS equivalents for GCG programs

[Derek Gatherer]

Hi

The following is a description from the GCG manual of the GCG program Gap:

Gap makes an alignment to find the maximum similarity between two sequences 
by the method of Needleman and Wunsch (J. Mol. Biol. 48; 443-453 (1970)) 
that is similar to finding the minimum difference according to the method 
of Sellers (SIAM J. of Applied Math 26; 787-793 (1974)). Smith, Waterman, 
and Fitch (J. Mol. Evol. 18; 38-46 (1981)) showed that the methods were 
precisely equivalent when the Needleman and Wunsch gap creation penalty is 
equal to the Sellers gap creation penalty - 0.5 and when the end gaps for 
Needleman and Wunsch are penalized in same way as all the other gaps. 
-ENDWeight allows you to penalize the end gaps introduced by Gap.

I have to confess, I'm a bit baffled by this.  Obviously, EMBOSS needle 
would do a NW alignment, but the gap opening penalty default in needle is 
10 and the gap extension is 0.5.  I'm not sure what is implied in Gap by 
"gap creation", or whether or not needle allows any end gap 
penalties.  Does anybody have any particular recommendations about the 
appropriate needle parameters to use to emulate Gap's behaviour?

I'm also looking for an equivalent of the GCG program Diverge, that 
calculates Ka/Ks values.  I think there is no equivalent to this in EMBOSS, 
but I may have missed something?

Cheers
Derek