Parsing Paralogs

Question

[Barby]

Hi there,

does anyone knows how I can parse paralogs in a newick tree, please?

[Michael Kuhn]

Can you please clarify your question a bit: What is your input? Can you provide an example?

Answer 1

[Javier Herrero]

Using Fitch's definition, any two genes related by a duplication event are paralogs. We can classify them into within-species paralogs (two genes in the same species) and between-species paralogs (two genes in different species). You will find a longer explanation and examples at http://www.ensembl.org/info/docs/compara/homology_method.html

If you are interested in within-species paralogs, the solution is pretty straightforward. By definition, any two genes in your tree that belong to the same species are paralogs.

Between-species paralogs (paralogous genes in different species) are more complicated to infer. You need to reconcile the gene tree with a species tree first. You can use RAP (http://pbil.univ-lyon1.fr/software/RAP/RAP.htm) or ETE (http://ete.cgenomics.org/) for this. Once you have done this, you can go through all the duplication nodes and infer a paralogy relationship between any gene in one of the branches and any gene in the other branch.

Note that any phylogenetic package will build a tree with all the sequences that you have aligned. In other words, you are also relying on the sequence similarity search you (or someone else) have performed before. You may want to make sure that one of the two paralogues is not an outlier.

[Javier Herrero]

I see. Maybe you should post another question about the best way of rooting 1700 gene trees. It might be useful if you can provide some details about which species you are working with.

[Barby]

that's great thanks! I tried ETE (SO algorithm) but the problem is that I got about 1700 trees (nine taxa), with some of them that do not contain all species, so they are not rooted. And the script does not work for unrooted trees.