I'd like to use a quick RAxML phylogeny as a starting tree in BEAST, but I can't figure out how to produce RAxML trees without polytomies... since BEAST requires starting trees to be bifurcating.
Thanks!
Matt
Hi Matt,
as far as I know, the best scoring ML tree obtained by RAxML should not contain any polytomies. Maybe the branches that seem like polytomies are just really short?
Best,
MIchael
RAxML should produce a strictly bifurcating tree. However, there are other Problems if you try to implement a RAxML tree as starting tree into BEAST.
But there are several tutorials how to process a RAxML tree to use it for beast. So just google some tutorials, take the one which fits you best, calculate a fast RAxML and process the tree
Hi Matt, I agree with Michael, when I started working with RAXML I thought the same thing, why the polytomies?, but when I was editing the trees using Figtree I realized that this "polytomies" were because the branch lenght is to short in some cases and the trees seems to have polytomies, Greetings Matt! :)
Great, thanks for the advice everyone! I bet you are right about the short branch lengths, so it might be a BEAST problem... I'm terrible with R but will see if I can find a tutorial. Thanks again!!
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