vclust [feature request] AAI calculation

Thanks for the amazing tool!

The viral DNA code is very dynamic and has no repair mechanisms, therefore viruses quickly mutate. However, they should be conserved on the aminoacid level, because deleterious mutations will prevent viruses from replication inside the host.

This type of clustering will be more appropriate methodologically.

Jul 17 '24 11:07 valentynbez

Hi Valentyn,

Thanks for reaching out! You are absolutely right. With nucleotide-based sequence comparisons and clustering, we can only reliably group viruses into species, or genera at best.

The AAI feature is on our to-do list, but we can't provide an estimated time for its availability yet. In the meantime, you can calculate AAI with external software and use Vclust's component, Clusty, for clustering based on the obtained AAI values.

Thanks! Andrzej

Jul 18 '24 08:07 aziele

Thank you for vclust! I support the author's suggestion to add clustering based on AAI calculation. Furthermore, are there any implementations or recommended parameters for new viruses, where the 70% for genus and 95% for species thresholds don't work?

Oct 29 '25 01:10 SergeyBaikal