Database Indexing

Index a collection of genomes to use as a custom MiGA database to query an unknown genome against this database or search the genomes of the database against each other by calculating the all-vs-all AAI and ANI matrixes.

Use this application to fully process all the genomes in a collection and build a searchable database


A collection of genomes (assemblies), typically 10 or more.


  • Project type: Select the type of project depending on how closely related the genomes in your collection are. For genome collections from different taxa (e.g., collections of Metagenome-Assembled Genomes), select Genomes. For collections of closely related genomes (i.e., all from the same species or closely related species), select Clade.

  • Index method: Select the search engines for the all-vs-all distance estimation. We strongly recommend using the default, Fast, which uses Diamond-based AAI and FastANI. If you would like your results to be directly comparable to BLAST-based AAI and ANI, you should select Sensitive.