[BioSQL-l] Phylogeny module

[Hilmar Lapp]

(for some reason I forgot to post this earlier - apologies)

I committed the phylogeny module a couple of weeks ago that Bill Piel  
and I created at Phyloinformatics Hackathon (http:// 
hackathon.nescent.org) in December (biosql-phylodb-pg.sql).

This is an optional module - BioSQL will work perfectly well without  
it. (Unless - surprise - you want to store phylogenetic trees.)

Right now there is only a PostgreSQL version, but Jamie Estill, a  
student in our Google Summer of Code program, has created a MySQL  
version that he or I will commit too.

I've now also added comments and made a few rather small changes to  
the module's schema since the initial revision:

	- widened width of of tree.identifier to 32 chars
	- added column tree.is_rooted of boolean type
	- renamed column node.gene_id to node.bioentry_id

If anyone was using this module already, here's the migration script  
in PostgreSQL:

ALTER TABLE tree ALTER COLUMN identifier TYPE VARCHAR(32);
ALTER TABLE tree ADD COLUMN is_rooted BOOLEAN DEFAULT TRUE;
ALTER TABLE node RENAME COLUMN gene_id TO bioentry_id;

	-hilmar
-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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