Just maximum parsimony tree?

[Kristian Davidsen]

Hi,

I can't seem to find the answer to this simple question anywhere:

Can I use IQ-TREE to find an MP tree and/or a list of equally MP trees?

Since you are already making MP trees through libpll and using these as starting trees for various ML models I see no reason why it shouldn't be possible to just get an MP tree out in the end (of course after a necessary tree space search).

Look forwards to hear.

Thanks for great software,
Kristian

[Bui Quang Minh]

Hi Kristian,

That’s a good question. IQ-TREE constructs 100 starting trees using MP, which are based on heuristics implemented in libpll (technically: random stepwise addition plus subtree pruning and regrafting). Since no thorough tree search is performed here, I don’t recommend to use them.

In fact we have developed a separate version, which extends the IQ-TREE search strategy for MP. I will send you a link in another email.

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

[Tamara Dru]

Hi,

could you please also send me the link to the separate version that allows for finding an MP tree?

Thanks a lot in advance!

Best regards,

Tamara

[Bui Quang Minh]

Dear Tamara,

Your question came just in time ;-) We recently published a paper on this:

D.T. Hoang, L.S. Vinh, T. Flouri, A. Stamatakis, A. von Haeselerc, and B.Q. Minhc (2018) MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC Evol. Biol., 18, 11. 

http://dx.doi.org/10.1186/s12862-018-1131-3 

with a link for download and manual.

Let us know if you have any questions,

Cheers

Minh

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