[ensembl-dev] Very long branch lengths in Compara gene trees

[Matthieu Muffato]

Hi Greg

The gene trees are build with TreeBest, which ships in a version of 
PhyML, and PhyML has a few constants in it. One of them is the maximum 
branch length, and is 1e5.

I think you can indeed conclude that the gene or the group of gene under 
that long branch is not at the correct position in the tree. We are 
investigating re-inserting those genes with tools like RAxML-EPA (or others)

Hope this helps,
Matthieu

On 12/12/13 15:28, Greg Slodkowicz wrote:
> Hi Ensembl-dev
> I noticed that some of the branches in the gene trees are extremely long
> (10E5 to be exact). I was wondering what's the rationale behind setting
> such long branch lengths?  Does it indicate that whatever gene set came
> out of the upstream analysis couldn't be meaningfully placed on one
> phylogenetic tree?
>
> Best,
> Greg