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Created with Raphaël 2.2.018Feb171413121110765329Jan171413107230Dec201918171698653229Nov2827262523212015141323Oct144330Sep2523328Aug12510Jul942124Jun191817141312331May29272423222016151413924Apr179320Mar1514625Feb2019171411765432130Jan24221615141311109818Dec13328Nov222120923Oct326Sep2413106514Aug13109731Jul201918106229Jun115425May2327Apr2625242320191816131211105431Mar29282723222120181615141352128Feb27262322212015931Dec301328Nov6220Oct27Sep212030Aug292423221817161028Jul272625212013121110Documentation for HMM functionalitySCHWED-4512: Tell clang on macOS to ignore unknown GCC warningsGet rid of unused VAX conversion files.Fixe doption nameSCHWED-4612: Set OpenGL GL preferences, new Python module name for sip in check if sip is installed.SCHWED-4649: Enforce new policy to get rid of -L in CMake callsAdapt new C/ CXX_FLAGS into the CI YAML fileallow to adapt parameter defaults when adding transition pseudo countsgive control over tau parameter estimation in AddAAPseudoCountsSCHWED-949: Updated tests for non-standard amino acids.Fix doc typoBum copyright to 2020Fix/clarify use of old legacy doxygen docBump copyright to 2020allow to adapt parameter defaults in HMMScoreMerge branch 'python3_port' into hmm_scoremove null model pseudo counts into separate functionadd pseudo counts according to Angermueller et al. 2012SCHWED-4612: Remove a message from HHblits bindings test.SCHWED-4612: Update CI Yaml file.SCHWED-4612: Get rid of some Numpy warnings, move from np.matrix to np.array.SCHWED-4612: Get rid of some Numpy warnings, move from np.matrix to np.array, keeping the matrix variant as deprecated method.SCHWED-4612: Get rid of TMalign compiler warningsSCHWED-4382: Better logging for HHblitsSCHWED-4612: Reduce Numpy compilation warningsMerge branch 'python3_port' into hmm_scoreslightly relax dcd io unit testremove openmm density plugin which has always been experimental and was never thoroughly testedSCHWED-4612: Update CMake call for CI.SCHWED-4612: Dealing with the NumPy deprecation compiler warning.Python export for HMM algorithmhook up hmm algorithms in build systemalgorithm that calculates an HMM-HMM alignment score the hhblits wayAlgorithms to add pseudo counts to ProfileHandle objects which contain HMM informationadd support for hmm related data in ProfileHandleSCHWED-4612: Ignore warning about unused functions by GCC, while the functions are used by unit tests.SCHWED-4612: Fix warning on unused (static) function.SCHWED-4612: Remove use of deprecated function.SCHWED-4612: Get rid of '-Wmaybe-uninitialized' from Vec3Try to force C++11 for older compilers.