[Biopython] Taxonomic Classification tree

[Hilmar Lapp]

On Feb 9, 2013, at 11:53 PM, Vincent Davis wrote:

> On Sat, Feb 9, 2013 at 9:03 PM, Paulo Nuin <nuin at genedrift.org> wrote:
> 
>> All phylogenetic trees are based on taxa. 

This is not true. Phylogenetic trees are based on a character matrix. The rows in such a matrix are called OTUs. OTUs may or may not refer to a taxon; they could (and nowadays typically do) refer to a gene, a protein, a (part of a) genome, or some other nucleic acid or amino acid sequence. 

> Maybe but Taxonomic Classification is not based on phylogenetics.

Not strictly, but it aspires to be. I.e., species taxonomies aspire to group taxa together that are monophyletic. In practice this isn't always the case, but it's the idea, and is one reason why taxonomies change. 

> What I have is a list of organisms and their Taxonomic Classification. I want to build a tree based on only the Taxonomic Classification.

You can obtain this directly from the NCBI taxonomy:

http://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi

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