Good morgon!
I have a set of HBV mutants in a region where overlapping occurs between two genes (p2/s1, the s and the polymerase gene, which evolve independently as stated by Zaaijer et al., J Gen Virol 2007, 88, 2137). The SBP analysis gave me a possible breakpoint, but the complete analysis for recombinant was impossible (output: cAIC could not be applied to this alignment; it has too few sites for the number of sequences). So. I performed the analysis with only one tree and had quite good results in comparison with tree obtained by bootstrapped ML.
My questions are:
1. could the breakpoint reflect something due to overlapping?
2. How can i introduce in my analysis a correct restrain for the overlapping?
3. Evaluating the antigenic escape is the most important aim of this work: I have 107 sequences, exceeding the capacity of TOGGLE. Could I submitt to TOOGLE only 100 selected sequences without bias (e.g. eliminating the WT seq and those with dN/dS=1)? in this case can I use TOOGLE independently from the other classical analyses offered by Datamonkey (i.e. SLAC and FEL)?
Thank you in advance, especially for data i have already get.
Best wishes.  
Anna Giulia

Hi, Sergei,
I apologize I did not answer earlier: after receiving your suggestions I was unable to use the server, for one of those strange tinks happening in the net - sometimes.
Today I have finally done Toggle: thank you very much for having improved the capacity of your software!
Now I have planned to be brave enough and try to put the double code of my overlapping genes in some software, e.g. in HyPhy. If I have troubles, I will return again to ask your help, Thanks!
(I am looking in the middle of the two genes).

Best wishes.
Anna Giulia