Skipping optimisation of candidate tree set

[kr3118]

Hi all,

I realised for some datasets, optimisation of the candidate tree set does not happen (it goes straight to UFBoot refinement stage). The only thing that is different is the input MSA and the resulting difference is either no optimisation or 100s of iterations in optimisation of the candidate tree set. Is this behaviour because IQTREE thinks no further optimisation will find a better tree?

I found that this happens on both v 2.3.6 and for 3.0.0.

I did change some of the default tree search settings: -ninit 1000 -ntop 100 -nbest 20, if this makes a difference.