Documentation for Databases

Geolocation Files

All Geolocation information was downloaded from Genomes.org, specifically the allCountries.zip found here.

The following steps are done to make the final files used:

1. unzip allCountries.zip && mv allCountries.txt allCountries_<download_date>.txt
2. python phylophoenix/bin/split_geonames.py --input allCountries_<download_date>.txt Note that this script will take several mins.
3. Compress the files with

for file in *_geolocation_20250707.txt; do
    if [[ -f "$file" ]]; then
        echo "Compressing $file"
        xz "$file"
    fi
done

4. Move files to the ~/phylophoenix/assets/ folder