Question: combining phylogenetic trees into a consensus super Tree
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gravatar for Moses
6 months ago by
Moses70
united states/ Bloomingtion/ Indiana University Bloomington
Moses70 wrote:

Hi all,

I have around 50 unrotoed phylogenetic trees that are generated using FastTree from 51 different gene families coming from different number of species. Not all of my trees have the same number of leaf nodes. Some might have a few more some a few less.

I want to combine these trees into one consensus (the best one explaining all of them) and also while I do that I would also like to know which leaves of these trees are being mapped (matched) together. I have checked PAUP turns out its not free, I've been trying to work with mesquite but their wiki page is down and website is not being supported. Does anyone have any suggestions of how can I do this?

If let's say a leaf node is not present on one of the trees but present in the other I would like that leaf node to also be present in the final supertree.

Any advice would be appreciated. Thanks.

tree phylogenetics • 328 views
ADD COMMENTlink written 6 months ago by Moses70

have you tried cegg.unige.ch/newick_utils ? what does it produce?

ADD REPLYlink written 6 months ago by Gabriel R.2.6k

There are several packages devoted to supertree reconstruction, see a list at https://omictools.com/supertree-construction-category .

One that I have seen cited more or less often is Clann

ADD REPLYlink written 6 months ago by h.mon27k

Thank you for this. I am looking into clann documentation now. Is it necessary for the program to know which leaf nodes match with each other aprioiri? In my case I just have many gene trees and I do not know which leaves are coming from which species in any of them, I just want to somehow do an optimal matching and construct a super Tree.

ADD REPLYlink written 6 months ago by Moses70
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