I am interested in downloading complete genomes to create a phylogenetic tree. The NCBI has a whole toolkit which they call Entrez Programming Utilities or eutils for short. (I found an EXCELLENT resource that walks me through everything I would need to know. Complete with a script in python to automate downloading these genomes off of NCBI.)
I have an "interesting-genomes.txt" file I'd like to find complete genomes for, HOWEVER this list of ID's contain the taxonomy identifier from uniprot ( ie http://www.uniprot.org/taxonomy/1000588).
For example, Streptococcus mitis bv. 2 str. SK95, has the corresponding taxonomy number of 1000588 in uniprot. In NCBI, it's ID is NC_013853.
I have a file containing a long list of taxonomy identifiers like 1000588, and not the NCBI ID's of NC_013853. Any ideas on how I can get around this?