I realised my question on "branch and bound" search for ML analysis could be misunderstood because I guess I mistranslated my french word in english. When I said that the exhaustive search led to a different tree with a slighty higher -Ln L value, I meant a better.
Branch and bound: 6h45mn, score:10745.09295
Exhaustive search: 47 mn, score: 10534.83665
(for info) Heuristic search: 24 mn, score: 10745.09295 (same topology as Branch and bound)
So I don't have a problem with the fact that the exhaustive search gave me a better tree but with such different computation times and final results.
I also would like to add one question about the HKY tests for competing topology. When I do it, I have some cases where the HKY test reject the hypothesis of no differences between 2 trees whereas a simple LRT test (with nbr of taxa -2 as the df) gives me strong support for difference. I read that HKY test is no good when there is an a priori that a topology is better than another, because this violates one of its parameter assumption. As my 2 topologies come from exhaustive search of separate analysis of mit. and nucl. sequences data I guess I have a strong a priori. However, I see very often such test used in the literrature with no much details about assumptions. So I just would like some advice about the range of application and confidence of both test to compare two competing topologies.
Thank you very much again,
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