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Why is --alt-ali disabled for nucleotide searches? #1123
Description
Hi there! I'm wondering why the --alt-ali flag is disabled in nucleotide mode.
// src/alignment/Alignment.cpp
if (altAlignment > 0) {
if (Parameters::isEqualDbtype(querySeqType, Parameters::DBTYPE_NUCLEOTIDES)) {
Debug(Debug::ERROR) << "Alternative alignments are not supported for nucleotides.\n";
EXIT(EXIT_FAILURE);
}We'd love to use mmseqs2 but this is a blocker for us. Is it just that it's never been implemented?
Curious to hear from you!
Activity
kimmanbo commentedon Oct 7, 2026
Hi @romanhaa !
Hope this answer is not too late.
I looked into the codebase, and there are some architectural challenges to implement additional local alignments on nucleotide search.
A few ideas come to my mind, but it will going to require heavy and serious testings and I'm not sure whether it's valid approach or not.
How about checking Riboseek?
Riboseek is sharing many modules from MMseqs2 and looks like it supports
--alt-aliunder certain conditions.