negative constraint tree search?

[Iker Irisarri]

Dear Minh & all,

I was wondering whether it is possible to conduct a negative constrained tree search in IQTREE, similar to using the -g option. By negative constraint I mean the best ML tree that does not contain a given bipartition (e.g. best ML where A and B are not monophyletic). If not, do you plan to implement it in the future?

Thank you very much for your time!

Iker

[Bui Quang Minh]

Dear Iker, 

That’s an interesting request - I haven’t thought about negative constraint before. Can you give a rationale behind such a feature, i.e. why do you think it is useful? Does it mean, for example, that you want to test the monophyly of A and B by comparing an unconstrained ML tree (where A and B are monophyletic) and a constrained ML tree (where A and B are not). And draw a conclusion if e.g. the 2nd tree is rejected.

Cheers, Minh

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Bui Quang Minh

Center for Integrative Bioinformatics Vienna (CIBIV)

Campus Vienna Biocenter 5, VBC5, Ebene 1

A-1030 Vienna, Austria

Phone: ++43 1 4277 74326

Email: minh.bui (AT) univie.ac.at

[Iker]

Hi,

Yes, exactly!

It is essentially the idea of a topology test, except that your unconstrained tree (null hypothesis) would have A+B as monophyletic and you want to compare this tree to the best ML where A+B are not monophyletic. This would tell you how much support there is for the monophyly of A+B, or give you the opportunity to compare site-likelihoods assuming or not this monophyly. I hope that makes sense.

Would be great to see such an option in IQTREE :-) Thanks!! All the best,

Iker

2017-10-03 15:06 GMT+02:00 Bui Quang Minh <minh...@univie.ac.at>:

Dear Iker, 

That’s an interesting request - I haven’t thought about negative constraint before. Can you give a rationale behind such a feature, i.e. why do you think it is useful? Does it mean, for example, that you want to test the monophyly of A and B by comparing an unconstrained ML tree (where A and B are monophyletic) and a constrained ML tree (where A and B are not). And draw a conclusion if e.g. the 2nd tree is rejected.

Cheers, Minh

On Oct 3, 2017, at 2:43 PM, Iker Irisarri <irisar...@gmail.com> wrote:

Dear Minh & all,

I was wondering whether it is possible to conduct a negative constrained tree search in IQTREE, similar to using the -g option. By negative constraint I mean the best ML tree that does not contain a given bipartition (e.g. best ML where A and B are not monophyletic). If not, do you plan to implement it in the future?

Thank you very much for your time!

Iker

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[des...@amnh.org]

dear minh and iker

did the negative tree constraint option get implemented in any available version of IQtree?

There is a second reason to implement it, be it rather esoteric and that is it is needed to obtain partitioned likelihood measures.

congrats on developing an awesome program.

Rob desalle

[Minh Bui]

Hi Rob,

Thanks for your interest. This feature is however not available. While it may sound simple from user perspective, the coding is actually challenging. Unless the implementation leads to a publication.

Cheers

Minh

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