Phylogenetic tree based on orthofinder results

Question

[Mehmet]

Dear All,

I have run orthofinder then trees_MSA to get gene trees, and it produced hundreds files. according to orthofinder manual, it says that gene trees can be used in some programs to visualize results. I would like to ask you, which gene trees should be used and how? I mean results in "gene trees" directory or "Trees" directory? Besides, do I need to combine all trees to make a single tree?

Best

Answer 1

[Sergey Naumenko]

Hi, Mehmet!

It depends on what do you want to study. If you need to infer a species tree, the best way is to concatenate all the alignments into one and run a program like Raxml or MrBayes. Then you will have just one species tree, perhaps with bootstrap values if you need them, and you can visualize the tree with Dendroscope. Not sure, why the main Dendroscope link is not working, you may try the other one Dendroscope2. Gene trees are trees inferred from individual genes. It is a different story - to compare gene trees and a species tree. Read more about phylogenetics in Phylogenetics handbook.

Sergey

[Mehmet]

Hi Sergey,

Thank you very much. This is very useful comment.

Answer 2

[david_emms]

Hi

OrthoFinder produces a gene tree for each orthogroup, this means you get gene trees for all your genes in all your species. These trees show how each gene is related to its orthologues and recent paralogues (paralogues that diverged since the last common ancestor of your set of species). It also produces a species tree showing how your species are related.

To visualise them, use Dendroscope as suggested by Sergey or http://etetoolkit.org/treeview/ is a good online tool.

All the best

David