[ensembl-dev] TreeBEST-compatible species tree

[Greg Slodkowicz]

Dear developers,
I was wondering if there is a way to access the species tree that is used for running TreeBEST? I have the ’normal’ Newick species tree from the Compara GitHub repository but it seems like TreeBEST is quite picky about the labelling of the tree nodes. 

What I would like to do is re-run gene-species tree reconciliation for a few gene trees of interest, get bootstrap replicates for that tree and then run some downstream analysis on them to get a measure of uncertainty introduced by the differences in the tree.I would ideally like the species tree from an archival (release 78) version of Ensembl (though I imagine it hasn’t changed that much).

Many thanks,
Greg 
-- 
Dr Greg Slodkowicz
Structural Studies (Babu Group)
MRC Laboratory of Molecular Biology
Francis Crick Avenue,
Cambridge, CB2 0QH, UK

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