[Biopython] Taxonomic Classification tree

[David Winter]

Hi Vincent,

It would probably be possible to do this with Biopython, either by

(a) searching the NCBI's taxonomy database with Eutils to get IDs, then 
fetching the corresponding taxonomy records and extracting the complete 
lineage for each of your taxa. You could find the "lowest shared taxon" 
for each one an build a tree

(b) Read the whole NCBI taxonomy using Phylo, and extracting a subtree 
with just your taxa

Both those are probably more work than you need to do though. The 
Interactive Tree of Life page (http://itol.embl.de/other_trees.shtml) 
can take taxon names or IDs and return a phylogeny.

You should be aware - taxonomy is a dynamic science, and assignments can 
change. The NCBI taxonomy is curated by people that know what they're 
talking about, but it's not a definitive tree of life or the result of a 
particular phylogenetic analysis.

David



--
David Winter
Research Associate
Allan Wilson Centre for Molecular Ecology and Evolution
Univeristy of Otago
Dunedin
New Zealand/ Aotearoa

ph + 64 22 018 0449
w: www.david-winter.info
blog: sciblogs.co.nz/the-atavism


On 2/10/2013 6:01 PM, Fields, Christopher J wrote:
> On Feb 9, 2013, at 10:53 PM, Vincent Davis <vincent at vincentdavis.net>
>   wrote:
>
>> On Sat, Feb 9, 2013 at 9:03 PM, Paulo Nuin <nuin at genedrift.org> wrote:
>>
>>> All phylogenetic trees are based on taxa. You might need to be more
>>> specific.
>>
>>
>> Maybe but Taxonomic Classification is not based on phylogenetics.
>> What I have is a list of organisms and their Taxonomic Classification. I
>> want to build a tree based on only the Taxonomic Classification.
>>
>> Vincent Davis
>> 720-301-3003
>
>
> There's code floating around on the bioperl side for doing this sort of thing, not sure if biopython has anything along these lines (I would be surprised if someone hasn't done this yet, though).
>
> chris
>
>
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