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HHsuite v3.1.0
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@martin-steinegger martin-steinegger released this 26 Feb 19:55
· 149 commits to master since this release
v3.1.0
4ef7751

Breaking changes:

  • hhmake requires an output file with -o (-o stdout is also valid). Previously, omitting an output would truncate the stdout output to 1000 lines, possibly resulting in corrupted files
  • make install is now required to place all HH-suite binaries in one location
  • Dropped support for global .hhdefaults configuration file
  • Documentation has moved to our GitHub Wiki

Features:

  • Added hhsearch_omp, hhsearch_mpi, hhalign_omp and haling_mpi binaries
  • Added -maxseq parameter. HH-suite does not need to be recompiled anymore to change the (now gone) MAXSEQ constant
  • Removed HHLIB environment variable from most tools (some old Perl scripts might still try to read it)
  • FFindex is now part of the HH-suite, no more submodule calls are needed
  • Dockerfile and docker images under soedinglab/hh-suite
  • Removed non-GPLv3 compatible code
  • hhalign can align multiple template files. Thanks @al42and

Bugfixes:

  • The HH-suite does not require SSSE3 anymore, SSE2 is sufficient. (But AVX2 is preferred with up to 2x speedup)
  • HHblits and HHsearch don't produce empty alignments anymore
  • ffindex_apply_mpi will not crash anymore on systems with low amount of virtual memory
  • hhblits_omp no longer has a max thread limit (it will however eventually run into IO issues)
  • HHsearch does not mention prefiltering in its output anymore
  • All parallelized tools will read their databases linearly if possible
  • HH-suite compiles without issues on GCC 4.8 and Clang 3.6 again
  • OpenMP and MPI parallelized tools will not create stray .hhr files anymore
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