[ensembl-dev] newick

Matthieu Muffato muffato at ebi.ac.uk
Tue Apr 14 12:34:30 BST 2020

Dear Joseph

The "left_index" and "right_index" columns are there to implement the 
Nested set model (cf https://en.wikipedia.org/wiki/Nested_set_model ). 
They allow quick retrieval of ancestors / descendants.

That said, if you want to export one of our speices-trees into, I would 
suggest to directly download them from the FTP 
ftp://ftp.ensembl.org/pub/release-99/compara/species_trees/, or use the 
Perl script ensembl-compara/scripts/examples/species_getSpeciesTree.pl


On 10/04/2020 10:29, Joseph Steinberger wrote:
> Dear Community -
> How do I process a mysql /*species*/ tree table in order to create a 
> newick file?
> I would like to generally understand what 'left index' and 'right 
> index' mean, as I think I can then process the table into a newick file.
> Thank you for your time -
> Yossi
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Matthieu Muffato, Ph.D.
Ensembl Compara Principal Developer
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room  A3-123
Phone + 44 (0) 1223 49 4631
Fax   + 44 (0) 1223 49 4468

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