[ensembl-dev] Huge branch lengths in gene trees

[Javier Herrero]

Dear Sébastien

Indeed, that is an upper branch length limit set by TreeBeST. This 
family is especially difficult to resolve as it contains essentially 3 
types of genes: full length, N-terminal part only or C-terminal part 
only. As such, many pairs of genes do not overlap at all in the 
alignment. As you can imagine, it is very difficult for the phylogenetic 
reconstruction algorithm to address these families.

We are working on a couple of developments that might help in those 
situations. We will let you know more if we make any progress.

Javier


On 16/10/12 15:29, Moretti Sébastien wrote:
> Hi
>
> I found some gene trees that have huge branch lengths:
> e.g. tree ENSGT00560000076605, gene ENSCJAG00000001973
> The branch leading to that gene/leaf is  100000  long.
> http://www.ensembl.org/Callithrix_jacchus/Gene/Compara_Tree?g=ENSCJAG00000001973;r=ACFV01174532.1:4628-45447;t=ENSCJAT00000003772 
>
>
> What does it mean ?
> Is it an upper branch length limit ?
>
> Thanks
>

-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK