Clarification on --ext Extension Modes for Incremental Cluster Expansion

[linweiliarchaea]

Dear Dr. Buchfink @bbuchfink,

We would like to extend an existing sequence cluster database by adding new query sequences, without reclustering the entire dataset from scratch.

In this context, we were wondering whether this use case is related to the --ext option (extension mode: banded-fast, banded-slow, or full). Specifically, could you clarify:

Whether any of these extension modes are intended to support incremental extension of existing clusters with new query sequences; and

What the conceptual and practical differences are among the banded-fast, banded-slow, and full extension modes, particularly in terms of sensitivity, computational cost, and suitability for cluster extension.

Any guidance on best practices for this scenario would be greatly appreciated.

Thank you very much for your time and for developing and maintaining this excellent tool.