[Biopython] Taxonomic Classification tree

[Paulo Nuin]

On 2013-02-13, at 11:30 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> 
> 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. 
> 
>> 

Around the gene, protein, sequence, phenotipic  character there's an OTU, and there's a a taxon. If you are analyzing extraterrestrial species (or car colours, or fridge models) you might not have a taxon on your OTU but otherwise each and every piece of data you analyze has come from a species, known or not, repeated or unique in your rows. Semantically, you are correct, but even if you put 1000 genes from the same species in a matrix, and generate a phylogenetic tree, you still based your tree on a taxon. 

P




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