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MMseqs2 Release 16-747c6

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@milot-mirdita milot-mirdita released this 26 Nov 13:16
· 9 commits to master since this release
16-747c6
747c64c

MMseqs2 Release 16 introduces support for GPU-accelerated searches [1]. Additionally, we fixed numerous bugs and relicensed MMseqs2 under the MIT license.

[1] Kallenborn F, Chacon A, Hundt C, Sirelkhatim H, Didi K, Dallago C, Mirdita M, Schmidt B, Steinegger M: GPU-accelerated homology search with MMseqs2. bioRxiv (2024).

Breaking Changes

  • Custom substitution matrices (--seed-sub-mat, --sub-mat) are not supported in this release. Only the built-in matrices will work. We will restore support in the next release. (93b2d94)

New Features and Enhancements

  • Added GPU support to MMseqs2, allowing for faster computations of sensitive alignments on CUDA-compatible hardware on the Turing generation or newer (a66ad0c, 81171a5, 1806c0c)
  • Added full-length six-frame translated search with --translation-mode 1 (#885)
  • Implement qframe and tframe output fields in convertalis (#615, #803, 417f22f)
  • Allows resuming of interrupted downloads in databases and createtaxdb (0b27c9d)
  • MMseqs2 taxonomy now always keeps at least the longest open reading frame within each input sequence after fragment elimination (#832, 5b4c816)
  • Added option to not compress outputs in tsv2exprofiledb (a146887)
  • filterdb has learned a new sort mode (--sort-entries 4 --weights file) to sort by priority (54f8983)
  • Updated tantan (3e53eee)

Bug Fixes

  • prefilter could use excessive memory and crash for highly redundant databases (950342d)
  • prefilter was not properly evaluating the last potential hit, increases sensitivity of k-mer prefilter slightly (06f7429)
  • result2msa works correctly with clustered clustered databases (78ae2c5)
  • Fixed ppos output field calculation in convertalis (fb38b7d, 816c5c9)
  • Fixed wrong coverage being passed to realignment (6267ffb)
  • Fixed --taxon-list being broken in multi-threaded prefilter and ungappedprefilter (804bb2a)
  • Fixed segmentation fault in prefilter (#872, a64d60a, ef2ebe9)
  • Fixed inconsistent ordering issue in createclusearchdb (b59ad53)
  • Corrected backtrace in SAM output for nucleotide-protein alignments and show reverse complement sequence correctly (#845, 5f23f1f)

Developer Notes

  • Disabled nedmalloc due a OpenMP crash in Cygwin (c498f51)
  • Breaking changes in how (sub)project command initialization works (1c08685, af2cc52)
  • Removed gzstream (111d893)
  • Breaking fix for parameter singleton in subprojects (5c6e32c)
  • Export MMSEQS_ARCH in CMakeCache for subprojects to use (48f13f9)
Assets 12
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