Failure to converge

[Torben Nielsen]

I have been trying to build a tree for almost 3 months now. The tree has apparently been built, but the bootstrap calculations won't converge. It gets to the "end" and this happens:
BETTER TREE FOUND at iteration 271: -36284850.528
Iteration 280 / LogL: -36286365.961 / Time: 1037h:1m:13s (338h:10m:6s left)
Iteration 290 / LogL: -36291948.911 / Time: 1066h:33m:44s (298h:52m:18s left)
Iteration 300 / LogL: -36287081.830 / Time: 1098h:31m:0s (260h:48m:0s left)
Log-likelihood cutoff on original alignment: -36288285.878
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.967
NOTE: UFBoot does not converge, continue at least 100 more iterations

Is there a way of stopping this and getting something out?

Thanks.

[Minh Bui]

Hi Torben,

Can you tell me more about your data, like how many sequences and what is the alignment length?

The fastest way is to use -fast option coupled with the SH-aLRT test (e.g., -alrt 1000), instead of the UFBoot option. This will perform a fast tree search and assess branch supports with this test.

Cheers

Minh

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