Entering edit mode
7.8 years ago
ashish
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680
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?
That is kind of the point of a phylogeny. Similar proteins cluster together into family clades…
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/
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.
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.
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.
Hey thanks, I got it now.
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.