muffato at ebi.ac.uk
Tue Apr 14 12:34:30 BST 2020
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 -
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/
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
Phone + 44 (0) 1223 49 4631
Fax + 44 (0) 1223 49 4468
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Dev