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Why is --alt-ali disabled for nucleotide searches? #1123

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Why is --alt-ali disabled for nucleotide searches?#1123

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@romanhaa
romanhaa
opened on Jul 22, 2026

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!

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  1. kimmanbo commented on Oct 7, 2026

    @kimmanbo
    kimmanbo
    on Oct 7, 2026
    Contributor

    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-ali under certain conditions.

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