Issues

• macOS Apple Clang: no-OpenMP build fails with duplicate mangled template definitions, while OpenMP is not detected automatically

  soedinglab/MMseqs2#1135 · Filter by author kimmanbo opened on Sep 22, 2026

• Understandig mmseqs2 taxonomy failure

  soedinglab/MMseqs2#1131 · Filter by author saracargnelutti01-ops opened on Sep 9, 2026
  18

• Easy-search crashes during mult-iteration nucleotide searches

  soedinglab/MMseqs2#1128 · Filter by author zwmuam opened on Aug 18, 2026

• Latest of version of MMseqs2 with clusthash on conda

  soedinglab/MMseqs2#1127 · Filter by author samhorsfield96 opened on Aug 13, 2026
  1

• makepaddedseqdb thread imbalance on length-skewed databases

  soedinglab/MMseqs2#1125 · Filter by author murfalo opened on Aug 11, 2026

• Why is --alt-ali disabled for nucleotide searches?

  soedinglab/MMseqs2#1123 · Filter by author romanhaa opened on Jul 22, 2026

• easy-search splits perfect full-length nucleotide alignments into two contiguous HSPs unlike BLASTN

  soedinglab/MMseqs2#1116 · Filter by author mlarjim opened on Jun 30, 2026

• Possible Clustering discrepancy

  soedinglab/MMseqs2#1115 · Filter by author sanyalab opened on Jun 29, 2026

• mmseqs filterdb

  soedinglab/MMseqs2#1110 · Filter by author Amanda-Pinski opened on May 28, 2026

• easy-cluster create jibrish fasta file with gpu usage

  soedinglab/MMseqs2#1108 · Filter by author moriaarama opened on May 19, 2026

• scripts created by Search.cpp not executable i.e. blastpgp.sh

  soedinglab/MMseqs2#1106 · Filter by author erpadmin opened on May 12, 2026

• Alignments extending into non-homologous regions in cluster and linclust

  soedinglab/MMseqs2#1104 · Filter by author alephreish opened on May 6, 2026

• Requesting to create a mmseq compatible RVDB prot 31.0 database.

  soedinglab/MMseqs2#1103 · Filter by author BasudevG opened on Apr 24, 2026
  1

• How to cluster almost 6 billion protein sequences?

  soedinglab/MMseqs2#1100 · Filter by author chrisAta opened on Apr 13, 2026
  7

• Is there any recommended setting for clustering short peptide (8-20 mer) databases?

  soedinglab/MMseqs2#1098 · Filter by author AmirAsgary opened on Mar 30, 2026

• Looking for a way to get the best match implied in LCA determination

  soedinglab/MMseqs2#1097 · Filter by author Nino-git opened on Mar 27, 2026

• MMSeqs database creation

  soedinglab/MMseqs2#1095 · Filter by author sanyalab opened on Mar 27, 2026

• MMSeqs2 splits alignment into two segments

  soedinglab/MMseqs2#1094 · Filter by author prototaxites opened on Mar 25, 2026

• wiki clarification

  soedinglab/MMseqs2#1090 · Filter by author OH-AU opened on Mar 17, 2026

• Searching only forward frames with translated search

  soedinglab/MMseqs2#1080 · Filter by author johnne opened on Feb 25, 2026

• about -c coupled with --num-iterations

  soedinglab/MMseqs2#1078 · Filter by author juanjo255 opened on Feb 10, 2026

• Error: translatenucs step died (segfault)

  soedinglab/MMseqs2#1072 · Filter by author schorlton-bugseq opened on Jan 27, 2026

• Exploring GPU-Accelerated Search for Tens of Billions of Proteins in MMseqs2

  soedinglab/MMseqs2#1070 · Filter by author linweiliarchaea opened on Dec 28, 2025

• error2：Regarding the Search Function

  soedinglab/MMseqs2#1067 · Filter by author ATPasepoly opened on Dec 7, 2025
  7

• GPU easy-cluster and easy-linclust write out ASCII headers but binary sequences to _rep_seq.fasta

  soedinglab/MMseqs2#1063 · Filter by author jecorn opened on Nov 26, 2025
  2