Question: infer sub-families from phylogenetic tree
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gravatar for ashish
2.0 years ago by
ashish200
ashish200 wrote:

I have a phylogentic tree representing a family of sequences. Now how do I identify sub-families in it. The proteins do not show much difference in their domain distribution. Is there any tool to cluster similar proteins into sub-families using a phylogenetic tree?

phylogeny • 732 views
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by ashish200
1

Is there any tool to cluster similar proteins into sub-families using a phylogenetic tree?

That is kind of the point of a phylogeny. Similar proteins cluster together into family clades…

ADD REPLYlink written 2.0 years ago by kloetzl1.0k

Yes that is fine. Take a look at this tree. These are all proteins belonging to one family. there are four sub-families in it. how do I mark those four subfamilies. https://postimg.org/image/l15u76r4f/

ADD REPLYlink written 2.0 years ago by ashish200

Depending on the tool you use to draw the phylogeny, you can mark special clades. For example, in figtree you can highlight clades by coloring them.

ADD REPLYlink written 2.0 years ago by kloetzl1.0k

I am not asking about coloring them. i want to know how do i determine the boundries these special clades. Did you see the image in the link? Can you tell me what are the boundaries of the for special clades in the image.

ADD REPLYlink written 2.0 years ago by ashish200
1

Can you tell me what are the boundaries of the for special clades in the image.

There is no definite answer to that. It depends on where you would like to cut off related sequences into distinct families. For that proper scaling would be required. There is no guarantee, for example that the two proteins on the bottom left are closer related to each other than to any leaf in the top right.

ADD REPLYlink written 2.0 years ago by kloetzl1.0k

Hey thanks, I got it now.

ADD REPLYlink written 2.0 years ago by ashish200

kloetzl is right, you already solved your problem. But you still have to inspect clusters, if you are uncertain about the tree you have you could make several trees and compute a consensus.

ADD REPLYlink written 2.0 years ago by Michael Dondrup45k
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