Considerations about choosing target sequences?

[xiaoyezao]

Hi HybPiper desinger,

Thanks for the great tool. I have some questions about the usage of target sequences. Given the following species tree:

X means a group of species that are close to A. The goal is to retrieve genes from X. Assuming that there are gene duplications after divergence of B and (A-X), and A and X, which is quite common in plants, the choice of target sequences will make a big difference:

1. using B as target reference, hybpiper will capture all homologs that are descent from the common ancestor AX.
2. using A as target reference, hybpiper will capture homologs derived from common ancestor of X, but will miss genes that duplicated before the A-X divergence.

Am I right? Can you comment on this?

Thank you,
Tao