biology as computational science
Cool, I worked with sqlalchemy and databases before, and it is interesting to see an application to a biological dataset. However, I am not very familiar with NCBI taxonomy... is it the taxonomy of all known species? Are there other datasets released with this system?Can I be of help in any way... are you planning on implementing other functionalities apart from the Newick tree function?
I think the NCBI Taxonomy is coupled with GenBank, so it should have all organisms for which something has been sequenced. It is, however, not a final source for the actual taxonomic tree, which is still changing (e.g. it doesn't have the "new animal phylogeny"). Currently, I have no plans to add other functionality -- I just needed to group species by the (approximate) taxonomy. But you're more than welcome to fork the code. ;-)
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