Features:

• Add pre merge back -premerge to improve contact prediction performance (see #205)
• Add SIMDe library to support ARM, PowerPC, and all kinds of SIMD standards

Breaking changes:

• cstranslate has no -b flag anymore

Features:

• Added new tab separated output format -blasttab
  Format: query target #match/tLen #mismatch #gapOpen qstart qend tstart tend eval score

Features:

• Fix compiler error in LLVM 8 to support bioconda

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

bugfixes:

• a3m.py
• hhmakemodel.py fixed by Hongbo Zhu
• userguide (fixed with user reports)
• renumberpdb.pl

feature:

• databases used by hhsuite do no longer require a cs219 ffindex database; and they require only an a3m or an hhm ffindex database not both