Looks up the location of sequences in genbank and adds it to a FASTA file. In this repo there is the bio-geolocation.py script, a demo jupyter notebook as well as unprocessed and processed files as an example. To use the script itself you'll need to invoke it with python3 and your .fas input file:
$ python3 bio-geolocation.py suillus.fas
Bio geolocation
extracting data from 104 sequences
getting geolocation data (this takes a while)
saving into processed.fas
done!
You will then have a nice processed.fas file.
You will need to sequence the genome and get an output from your lab. For example: Mushroom Observer observation with DNA sequence of a new species of Suillus.
Then BLAST is used to find closely related sequences. These are downloaded and then fed into the GenBank database to get the country.
All of this data is then used to generate phylogenetic trees
You will need python3 and pip as a prerequisite. Virtualenv is highly recommended to keep these packages away from messing around with your other packages.
pip install jupyter
jupyter notebook
open browser and go to Bio geolocation.ipynb
Probably write a server that accepts .fas files as uploads, and then renders it on a map.