# Clustering MiGA generates a clustering-based indexing of databases using ANI distances (for clade projects) or AAI distances (for all other projects). This indexing enables quick searching of databases with query genomes. ## General algorithm The AAI or ANI values are transformed to distances (1 - identity), and the all-vs-all distance matrix is used to generate a *k*-medoids partition (PAM: Partition Around Medoids). *k* is selected to simultaneously optimize for maximum Silhouette average width and minimum Silhouette negative area, between 2 and 100 (or the number of genomes minus 1, whichever is smaller). Once the partitions are defined, the same algorithm is applied recursively to each partition with 8 or more genomes. The resulting clustering-based indexing is used to speed-up query searches. In some cases, it can also be used as *de novo* typing scheme, in particular for ANI distances (clade projects). ## Genomospecies proposals In addition to the above clustering-based indexing, MiGA clusters genomes by Markov Clustering (MCL) using all ANI values above 95% as edges. The result is a collection of discrete genomospecies. The list of genomes per genomospecies is sorted by medoid-ranking, in which the first genome has the minimum average distance to all other genomes in the genomospecies. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://manual.microbial-genomes.org/part2/clustering.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.