Question: Tree rooting method
0
gravatar for bpz
4.0 years ago by
bpz60
Mexico
bpz60 wrote:

Hello

I have a phylogenetic tree composed of +1000 protein sequences, and I need to assign a root. Finding an outgroup is extremely difficult. I was wondering if anyone knows a way to assign a root without an outgroup (besides the midpoint rooting method).

Thanks for the help, cheers.

rooting outgroup phylogeny • 1.3k views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by bpz60

I wonder why having a root which is not phylogenetically significant. I mean, usually you use outgroups to root trees in order to have information on the evolutionary relationship amongst the the groups in your tree. Not using this approach means rooting just to have a "prettier" tree, i guess. So in my eyes the answer is use an un-rooted tree.

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by dago2.6k

A root gives a tree "polarity", it is indispensable if you need to calculate a molecular clock.

ADD REPLYlink written 4.0 years ago by bpz60

I think you are right, but what is the meaning of a root that does not have real evolutionary value?

ADD REPLYlink written 4.0 years ago by dago2.6k

That is why I need to find a method to get a root with evolutionary significance. (the midpoint root method probably won't work, for the reason you stated). I don't know if only the outgroup method provides a significant root.

ADD REPLYlink written 4.0 years ago by bpz60
0
gravatar for bpz
4.0 years ago by
bpz60
Mexico
bpz60 wrote:

Anyone?, Is there an alternative method?

ADD COMMENTlink written 4.0 years ago by bpz60
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