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 :)
On 06/06/2012 06:28 AM, yizi yang wrote:
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
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
Could you offer me any suggestion and information?
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
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.
offer me any suggestion and information?