454 amplicon sequencing - gene family with large number of paralogs

[qiwei]

Thanks for your interests. The problem was solved. The paralogs can be treated as known variants, since the 454 amplicon analyzer supports this functionality.

--------------------------
As requested, I re-posted the question I asked earlier (I didn't save the exact copy, just try my best to rewrite the question):
I am studying the association of genetic variations within a gene family to certain phenotypes, and is planning to speed up the screening process with 454 amplicon sequencing. But I don't know if I should treat each paralog as a reference sequence or as known variants. The paralogs are highly similar at sequence level, with a few point mutations and small indels.

[ECO]

Hi Wei,

In the future it would be great if you could leave your post here for others to reference, as someone will undoubtedly have the same question in the future.