[Biopython-dev] [Wg-phyloinformatics] GSoC Weekly Update 9: PhyloXML forBiopython

Peter biopython at maubp.freeserve.co.uk
Thu Jul 23 16:21:05 UTC 2009

On Thu, Jul 23, 2009 at 4:59 PM, Eric Talevich<eric.talevich at gmail.com> wrote:
> Question:
> The Node objects in PhyloDB have left_idx and right_idx attributes. It looks
> like nodes are being kept in a double-linked list, which seems like
> unusually low-level information to keep around since Perl, Python, Ruby and
> Java all have flexible array or list types that can keep track of element
> order efficiently. Is there a use for these indexes in general phylogenetics
> work that couldn't be handled by other language-specific constructs?

I would guess this is like the left/right indices used in BioSQL's taxon tree,
see http://www.oreillynet.com/pub/a/network/2002/11/27/bioconf.html
If they are being used the same way, the are an expensive to calculate
second indexing scheme, which is useful for many tree operations.


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