Constrained tree search

[bqminh]

Allowing users to supply a constraint tree topology (-g option) to guide tree search, such that the resulting tree obeys the constraint. A naive implementation will be released with version 1.5.0.

iqtree -s alignment -g constraint_tree ...

TODOs (as of Sept 8, 2016):

• Speed up the naive version, as it right now can be slow for large trees. This involves mainly two steps: the initial tree construction and the NNI moves.

[blackrim]

I like this feature. However, it is quite slow for larger trees (>500 tips). Any advice there?

[OlgaChern]

Hi Stephen, great to hear that you find this feature useful. So far we only have a naive version, which is indeed quite slow for large trees. The improvement of runtime for constrained search is on our agenda though at the moment cannot be precise about when we’ll release it. We’ll send out the suggestions for large trees within next days. Cheers, Olga

…

On 06 Apr 2017, at 02:38, Stephen Smith ***@***.***> wrote: I like this feature. However, it is quite slow for larger trees (>500 tips). Any advice there? — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#8 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APMHUt-MYHvzNLbOv0d-r1jrLsRNJRv7ks5rtDP_gaJpZM4J37_D>.

[blackrim]

Sounds good. thanks

[bqminh]

DONE.