Dear Sergei,

I ran GARD on 1200 alignments without any problem, except for one gene. The computation never stops, and I obtain the following error message:


Code (]Error:Constrained optimization failed, since a starting point within the domain specified for the variables couldn't be found. Set it by hand, or check your constraints for compatibility. Failed constraint:c_scale:=RS_1*PS_1+1*(1-PS_1)*PS_2+1*RS_3*(1-PS_1)*(1-PS_2)*PS_3+1*RS_3*RS_4*(1-PS_1)*(1-PS_2)*(1-PS_3) must be in [0,10000):

. Current value = 10000. Current BL Command:Optimize storing into, lf_MLES, the following likelihood function:lf ;

Any idea?
I can send the mysterious alignment if you want.

Thank you,
-Tristan

Dear Tristan,

This is an obscure condition which sometimes happens if the optimization algorithm fails to find a valid starting point (subject to parameter constraints). I'd like to see the alignment which gives the error, because this condition should not occur in GARD!

Cheers,
Sergei