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Created with Raphaël 2.2.020Apr171626Mar2319161163226Feb2524201918171413121110765329Jan171413107230Dec201918171698653229Nov2827262523212015141323Oct144330Sep2523328Aug12510Jul942124Jun191817141312331May29272423222016151413924Apr179320Mar1514625Feb2019171411765432130Jan24221615141311109818Dec13328Nov222120923Oct326Sep2413106514Aug13109731Jul201918106229Jun115425May2327Apr2625242320191816131211105431Mar29282723222120181615141352128Feb27262322212015931Dec30Documentation for HMM functionalityallow to adapt parameter defaults when adding transition pseudo countsgive control over tau parameter estimation in AddAAPseudoCountsallow to adapt parameter defaults in HMMScoremove null model pseudo counts into separate functionadd pseudo counts according to Angermueller et al. 2012Python 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 ProfileHandleMerge branch 'develop' into hmm_scoreadd 'bad interpreter' issue as cause to raise RuntimeErrorundo temporary depug output for CI investigationpseudo commit to trigger CI runexplicitely add perl to "add secondary structure" commandtemp committemp commitMerge branch 'develop' into hhblits3load HHblits 3 in ci ymlSet ss_pred and ss_conf to None if not available in a3m/hhm parsingrestore default of assigning secondary structurerelax strict ordering requirements of sspred, ssconf and sequencesadapt unit tests to HHblits 3adapt testfiles with slightly different content when derived from HHblits 3replace hhblits db used in unit tests - the new one can be read by HHblits 3document remote repositoriesSpelling beeUse a more verbose Docker image tagMerge branch 'master' into developMerge branch 'release-2.0.0'2.0.02.0.0Python export for estimating cbeta positionsadapt logging and raising behaviour in hhblits bindingmake blosum data reproducibleport to hhblits 3Fix bump-cersion script and Singularity fileMerge branch 'release-2.0.0' into developfix DeprecationWarning: invalid escape sequence2.0.0-rc12.0.0-rc1Fixed documentation being written to a hardcoded directorySCHWED-4637: Added version 2.0.0 to the changelog2.0.0-rc2.0.0-rc