Dealing with Null Alleles

[daniel...@gmail.com]

Hello everyone
I am tryint to run my microsatellite data on structure but I am encountering some dificulties...

My data has a high occurance of null allels, so to deal with that, I am using RECESSIVEALLELS=1 (as reccomended)...

However, to do that, I need an extra line on my table with information on which alleles are recessive.
I dont know which allele is recessive and therefore, on the recessive allele line on the table, I have written -9, for every marker

-9 is also the number I use as missing data...

The programme runs fine for K=1,2 and 3, but then it doesnt run anymore for K=4,5 and 6... and starts working again for K= 7+

Is there anyway to solve this?

To go around this problem, I have changed the values on the recessive line from -9 to -8 (since i dont have -8 anywhere on my data).... the programme now works for every value of K, but the results I am obtaining are quite different from what I was getting when my recessive allele values where the same as my missing data values...

which should be the "correct" values, the ones where my missing values and my recessive alleles (that i dont have information for) have the same value on the table, or when they have differen values?

thank you

[Adii_ (Institute of Genetics and Animal Breeding)]

How u can tell u got many null allels? and what do You mean by saying You do't know which allel is recesive? 

I guess, that You check Your data in some soft, Micro-checker?

Adii_