PCR contamination by recombination - (Jul/25/2005 )

Dear all,

I have been working with the same gene than does my lab partners. So, after phylogenetic analyses I detected a lot of clear contaminations in my samples (as shown by cluster intermingling). So, I decided to change to another genes...
The thing is that there are some samples that are negative for the new genes but for the "old" gene I have sequences that appear to be monophyletic but a little bit unique for each patient.

Do you think It would be possible the contamination of my PCR by intrapatient recombination?? If so, how do I test this?

I will really appreciate every response,

I am having a hard time understanding what you are try to do. Could you be more specific about what your problem is exactly?