Find corresponding branch from gene tree in species tree

Question

[Charlotte West]

I have constructed a gene tree for a single gene family across various species. The internal nodes of this tree represent gene duplication events and also speciation events. The leaves are individual genes of the gene families.

Say if I also have the corresponding species tree. How can I find the branch in the species tree that corresponds to any given branch in the gene tree? For example, say there is a duplication node in the gene tree I am particularly interested in, and I would like to find out where (on which branch) in the species tree this duplication event took place. How can I do that? And do the gene tree and species tree need to be completely reconciled in order to do this?

[andres.firrincieli]

check Notung: link

[Charlotte West]

Following your suggestion I've been playing around with Notung and seems like its got a lot of great features. I ran:

java -jar notung -g GENE_TREE.nhx -s SPECIES_TREE.nh --reconcile

And got the file GENE_TREE.nhx.reconciled. I also tried the --savepng option to have a look at the result. My original GENE_TREE.nhx has the duplication of interest labelled as [&&NHX:D=Y:retro=Y], where retro=Y is used to identify this node of interest. However I don't find retro=Y in the output file GENE_TREE.nhx.reconciled, nor have I seen a way to annotate the corresponding branch in the png. Any Idea how I can do this?

[andres.firrincieli]

I use the Notung's graphical user interface to display the duplication events and use a different software to highlight the nodes in the tree in which that event occurs.

[Charlotte West]

This is for a pipeline where I will process hundreds of trees, so I need a programmatic solution :)

[andres.firrincieli]

Well, good luck then ;)