[ensembl-dev] GeneGainLossTree

[Miguel Pignatelli]

Hi Ed,

The Gene gain/loss trees represent the phylogenetic history of the gene 
families in Ensembl under the species tree point of view. For each gene 
family we provide a species tree showing the number of genes in the 
extant species, an estimation of the number of genes in the ancestral 
states and the significant gene gains and losses events in the evolution 
of the gene family. These estimations are done using the CAFE software [1].
The relevant objects in our API are CAFEGeneFamily and CAFEGeneFamilyNode.

In rel75 we had a problem with the estimated number of members in the 
ancestral states not going through. This is fixed for rel76. If you want 
this data for 75 let me know.

Hope this helps,

M;

[1] http://bioinformatics.oxfordjournals.org/content/22/10/1269.full

On 23/05/14 18:42, Ed Gray wrote:
> Hi All,
>
> Another question that is tree related.  I see the idea of a
> GeneGainLossTree, but I'm not sure what object it relates to.  Any hint
> would be helpful.  There is scant information available via google on
> GeneGainLossTrees are they simply GeneTrees or something more
>
> Best and thanks greatly!
> Ed
>
> PS: I would be most honored to run code against a pre-release of R76 if
> you want some feedback. It helps me and maybe you.
>
>
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-- 

Miguel Pignatelli, PhD

Ensembl Developer - Comparative Genomics
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK
Room A3-33
Phone + 44 (0) 1223 494 598
Fax   + 44 (0) 1223 494 468