[Bioperl-l] Bio::DB::Taxonomy root not present

Hilmar Lapp hlapp at drycafe.net
Thu Jul 7 22:28:21 UTC 2011

On Jul 7, 2011, at 3:22 PM, Brian Osborne wrote:

> It's also true that having 5 trees instead of 1 is incorrect  
> scientifically

That's a strong statement and I'm not sure I agree with this - let's  
keep in mind that these are taxonomies, not phylogenetic trees of all  
of life. Not every taxonomy has a node for "all of life" or for LUCA.  
For example, ITIS, one of the most widely used taxonomies if you're  
not dealing strictly with molecular data, does not - there is one  
"tree" for each kingdom of life. (Not that I want to recommend that as  
a good thing.)

I agree with your programming awkwardness argument, though I would  
add  that looking for a specific label of a node to identify the root  
is always a bad (because fragile) thing to do. A better way to  
identify a root node would be parent undefined, or being the same as  
the node itself. If the code did that for each the 5 or so children of  
'root', then the fake root could be removed.

At the very least code in Bio::DB::Taxonomy or anywhere else should  
not assume that there is a single root for a taxonomy. Because there  
are taxonomies for which this really isn't the case.


: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :

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