How to cluster and filter gene clusters across many genomes to infer their distribution

[JoshPhd]

I am using Spacedust to analyze gene clusters across multiple genomes and would appreciate some guidance on downstream analysis and interpretation.

Specifically, I ran Spacedust using 100 genomes vs. 100 genomes and successfully obtained the clusters.tsv output. However, from my understanding of the results, the reported gene cluster matches are essentially 1 vs. 1 comparisons (i.e., pairwise matches between individual genomes).

What I would like to achieve next is a higher-level clustering and filtering of these gene clusters in order to answer questions such as: **Which types of gene clusters are shared across multiple genomes?**For example, identifying a gene cluster that appears to be present in ~10 out of the 100 genomes, rather than only interpreting pairwise matches.

Does Spacedust provide any built-in functionality or recommended workflow to merge or cluster pairwise gene cluster matches into higher-order groups?

Thank you very much for developing and maintaining Spacedust.