While working on a complete bacterial genome comparison/phylogenetic classification based on Maximum Unique Matches, I noticed that NCBI also shows some sub-species tree on their genome project pages (for example this one for a S. aureus genome).
I cannot find whether it is real full genome or based on a shared core-genome.
I also tried searching the forum as well as the documentation at NCBI but seem unable to locate how this tree was generated (to generate the distance matrix) with what kind of phylogenetic algorithm (NJ, ML, etc)?
Any pointers welcomed.
There is a worrisome disclaimer on the page called
How to reference the NCBI taxonomy database?
Based on this (see below) I would not expect any answers. It states:
The NCBI taxonomy database is not a primary source for taxonomic or phylogenetic information. Furthermore, the database does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts. Consequently, the NCBI taxonomy database is not a phylogenetic or taxonomic authority and should not be cited as such.
The tree in question is not from the NCBI Taxonomy: in the NCBI Taxonomy, the subspecies are not resolved at all http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1280 In the linked example, they are clustered, i.e. contain much more information than the NCBI Taxonomy.
Thanks guys. Missed that. Not that I wanted to use their trees...I was building my own from complete genomes and just encountered these and wondered how they were made... but I suspect they can be sourced from everywhere... Still strange it is not properly referenced anywhere...so what is its use?
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PS: no reaction from the "authors"/responsibles at NCBI (yet).
PPS: today still no details... first level contact "served me off" with non satisfactory answer last year...still waiting for details.