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Re: construct gene trees


fransua Jun 6, 2012 8:32 AM
Posted in group: The ETE toolkit
Hi Yizi,

Then, you have a species tree, and a set of orthologous genes from which your are able to generate a gene tree using phyml. ETE won't improve the topology phyml gives you, however you will be able to see quickly if the orthology/paralogy relationship is repected in your gene tree. Here there is a simple example on how to do this (you can forget about the part of the alignment "alg", it is not necessary for the tree reconciliation):
http://packages.python.org/ete2/tutorial/tutorial_phylogeny.html#visualization-of-phylogenetic-trees

(I do not know about TreeBest, but what they are showing in their frontpage, is very similar)

hope this helps :)

regards,

francois


On 06/06/2012 06:28 AM, yizi yang wrote:
Dear Jaime,

Thank you a lot for help!

I got some protein sequences expressed by orthologous genes from multiple species. These proteins are compared and grouped by OrthoMCL. I would like to infer the evolutionary history of these orthologous genes in the form of tree. I know that some gene trees can be constructed under the guide of associated species trees, since we know species phylogenies. Method used in



is one example of them, but I think it is a old program.

I also heard that some gene trees were built using PhyML with the help of ETE toolkit. It is easy for me to build a rooted tree using the latest version of PhyML, but I do not know how to improve tree topology under the guide of species phylogenies using ETE toolkit.

Could you offer me any suggestion and information?

Thanks again!

Yizi

2012/6/4 Jaime Huerta Cepas <jhu...@crg.es>
Hello Yizi, 

could you be a bit more specific about what you need? Orthology & paralagy prediction, programmatic rooting, relative node dating...? Or perhaps you just want to learn how load newick trees into python Tree objects. Please, let us know a bit more about your problem so we can try to help you. 

cheers, 

Jaime

On Sat, Jun 2, 2012 at 6:23 PM, yizi yang <yangy...@gmail.com> wrote:
Hi, everyone

Thanks a lot for help.

I would like to construct gene trees for orthologous gene. Some rooted
trees are built using Phyml. These trees will be exported to ETE for
gene trees. However  I do not know how to handle it. Could anyone
offer me any suggestion and information?

Best Regards

Yizi