[Bioperl-l] get_lca method very slow on many nodes

Sendu Bala bix at sendu.me.uk
Mon Aug 11 17:44:37 UTC 2008

Gabriel Valiente wrote:
> Despite the speedup for merge_lineage, the get_lca method still runs 
> very slow on a large number of nodes (say, 1500 nodes) and it does not 
> rely on merge_lineage. In the get_lca method, all the lineages are first 
> collected in @paths in order to later find their $lca, while it might be 
> faster to process each $path as soon as it is obtained with the 
> get_lineage_nodes method.

If you try that idea out and it works, please do commit it. I've no 
further suggestions atm, but I haven't had a chance to look at it to 
remind myself what happens.

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