├── AUTHORS ├── BUILD_and_INSTALL__GPU__unix.sh ├── BUILD_and_INSTALL__GPU__unix__Hopper.sh ├── BUILD_and_INSTALL__GPU__unix__clang.sh ├── BUILD_and_INSTALL__GPU__win64.cmd ├── BUILD_and_INSTALL__mp__unix.sh ├── BUILD_and_INSTALL__mp__unix__clang.sh ├── BUILD_and_INSTALL__mp__win64.cmd ├── CITATION.cff.obs ├── ChangeLog ├── GTalign_demo.ipynb ├── GTalign_demo_search.ipynb ├── LICENSE.md ├── Linux_installer_GPU ├── GTalign-linux64-installer-GPU.sh └── bin │ └── gtalign ├── Linux_installer_mp ├── GTalign-linux64-installer-mp.sh └── bin │ └── gtalign ├── MS_Windows10_installer_GPU └── GTalign-win64-installer.msi ├── README.md ├── VERSION ├── imgs ├── gtalign_examples_m.jpg ├── gtalign_header.jpg └── gtalign_header.jpg.obs ├── out ├── 2021-09-18_00000039_1__0.md └── gtalign_options.md └── src ├── CMakeLists.txt ├── extzlib ├── CMakeLists.txt ├── LICENSE ├── adler32.c ├── compress.c ├── crc32.c ├── crc32.h ├── deflate.c ├── deflate.h ├── gzclose.c ├── gzguts.h ├── gzlib.c ├── gzread.c ├── gzwrite.c ├── infback.c ├── inffast.c ├── inffast.h ├── inffixed.h ├── inflate.c ├── inflate.h ├── inftrees.c ├── inftrees.h ├── trees.c ├── trees.h ├── uncompr.c ├── zconf.h ├── zlib.h ├── zutil.c └── zutil.h ├── gtalign ├── CMakeLists.txt ├── gtalign.cpp └── gtalign.h ├── incconf └── localconfig.h ├── libgenp ├── CMakeLists.txt ├── gdats │ ├── DRDataDeleter.h │ ├── FlexDataRead.cpp │ ├── FlexDataRead.h │ ├── InputFilelist.cpp │ ├── InputFilelist.h │ ├── PM2DVectorFields.cpp │ ├── PM2DVectorFields.h │ ├── PMBatchStrData.cpp │ ├── PMBatchStrData.h │ ├── PMBatchStrData.inl │ ├── PMBatchStrDataIndex.cpp │ ├── PMBatchStrDataIndex.h │ ├── TdDataReader.cpp │ ├── TdDataReader.h │ └── gdconst.h ├── goutp │ ├── TdAlnWriter.cpp │ ├── TdAlnWriter.h │ ├── TdAlnWriterJSON.cpp │ ├── TdAlnWriterPlain.cpp │ ├── TdClustWriter.cpp │ ├── TdClustWriter.h │ ├── TdFinalizer.cpp │ ├── TdFinalizer.h │ ├── TdFinalizerJSON.cpp │ └── TdFinalizerPlain.cpp └── gproc │ ├── btckcoords.h │ ├── dputils.h │ └── gproc.h ├── libmycu ├── CMakeLists.txt ├── cubatch │ ├── CuBatch.cu │ ├── CuBatch.cuh │ ├── TdCommutator.cpp │ └── TdCommutator.h ├── cucom │ ├── cucommon.h │ ├── cudef.h │ ├── cugraphs.cuh │ ├── cutemplates.h │ ├── cutimer.cuh │ ├── myassert.h │ ├── myatomic.cuh │ ├── mysort.cuh │ └── warpscan.cuh ├── cudp │ ├── btck2match.cu │ ├── btck2match.cuh │ ├── constrained_btck2match.cu │ ├── constrained_btck2match.cuh │ ├── dpagc_ssw_btck_specscore.cu │ ├── dpagc_ssw_btck_specscore.cuh │ ├── dpagc_tfm_ssw_btck_specscore.cu │ ├── dpagc_tfm_ssw_btck_specscore.cuh │ ├── dpss.cu │ ├── dpss.cuh │ ├── dpsslocal.cu │ ├── dpsslocal.cuh │ ├── dpssw_btck.cu │ ├── dpssw_btck.cuh │ ├── dpssw_btck_specscore.cu │ ├── dpssw_btck_specscore.cuh │ ├── dpssw_tfm_btck.cu │ ├── dpssw_tfm_btck.cuh │ ├── dpw_btck.cu │ ├── dpw_btck.cuh │ ├── dpw_btck_specscore.cu │ ├── dpw_btck_specscore.cuh │ ├── dpw_score.cu │ ├── dpw_score.cuh │ ├── production_match2aln.cu │ └── production_match2aln.cuh ├── cudp2 │ ├── dpw_btck_complete.cu │ └── dpw_btck_complete.cuh ├── cufilter │ ├── coverage.cu │ ├── coverage.cuh │ ├── reformatter.cu │ ├── reformatter.cuh │ ├── similarity.cu │ └── similarity.cuh ├── culayout │ ├── CuDeviceMemory.cu │ ├── CuDeviceMemory.cuh │ └── cuconstant.cuh ├── cumath │ └── cumath.h ├── cuproc │ ├── Devices.cu │ ├── Devices.h │ ├── JobDispatcher.cpp │ ├── JobDispatcher.h │ ├── cuprocconf.cpp │ └── cuprocconf.h ├── cuss │ ├── cusecstr.cu │ ├── cusecstr.cuh │ ├── ssk.cu │ └── ssk.cuh ├── custage1 │ ├── custage1.cu │ ├── custage1.cuh │ ├── custage2.cu │ ├── custage2.cuh │ ├── custage_fin.cu │ ├── custage_fin.cuh │ ├── custage_frg3.cu │ ├── custage_frg3.cuh │ ├── custage_ssrr.cu │ └── custage_ssrr.cuh ├── custages │ ├── covariance.cu │ ├── covariance.cuh │ ├── covariance_dp_refn.cu │ ├── covariance_dp_refn.cuh │ ├── covariance_dp_scan.cu │ ├── covariance_dp_scan.cuh │ ├── covariance_plus.cu │ ├── covariance_plus.cuh │ ├── covariance_refn.cu │ ├── covariance_refn.cuh │ ├── covariance_swift_scan.cu │ ├── covariance_swift_scan.cuh │ ├── fields.cuh │ ├── fragment.cuh │ ├── scoring.cu │ ├── scoring.cuh │ ├── stagecnsts.cuh │ ├── transform.cu │ └── transform.cuh ├── custages2 │ ├── covariance_complete.cu │ ├── covariance_complete.cuh │ ├── covariance_dp_refn_complete.cu │ ├── covariance_dp_refn_complete.cuh │ ├── covariance_fin_dp_refn_complete.cu │ ├── covariance_fin_dp_refn_complete.cuh │ ├── covariance_production_dp_refn_complete.cu │ ├── covariance_production_dp_refn_complete.cuh │ ├── covariance_refn_complete.cu │ ├── covariance_refn_complete.cuh │ ├── production_2tmscore.cu │ └── production_2tmscore.cuh ├── custgfrg │ ├── linear_scoring.cu │ ├── linear_scoring.cuh │ ├── linear_scoring2.cu │ ├── linear_scoring2.cuh │ ├── local_similarity0.cu │ ├── local_similarity0.cuh │ ├── local_similarity02.cu │ └── local_similarity02.cuh └── custgfrg2 │ ├── linear_scoring2_complete.cu │ └── linear_scoring2_complete.cuh ├── libmymp ├── CMakeLists.txt ├── mpbatch │ ├── MpBatch.cpp │ └── MpBatch.h ├── mpdp │ ├── MpDPHub.cpp │ ├── MpDPHub.h │ └── mpdpbase.h ├── mpfilter │ ├── MpReform.cpp │ └── MpReform.h ├── mplayout │ ├── MpGlobalMemory.cpp │ └── MpGlobalMemory.h ├── mpproc │ ├── TaskScheduler.cpp │ ├── TaskScheduler.h │ ├── mpprocconf.h │ └── mpprocconfbase.h ├── mpss │ ├── MpSecStr.cpp │ └── MpSecStr.h ├── mpstage1 │ ├── MpStage1.cpp │ ├── MpStage1.h │ ├── MpStage2.h │ ├── MpStageBase.cpp │ ├── MpStageBase.h │ ├── MpStageFin.cpp │ ├── MpStageFin.h │ ├── MpStageFrg3.cpp │ ├── MpStageFrg3.h │ └── MpStageSSRR.h ├── mpstages │ ├── covariancebase.h │ ├── linearscoringbase.h │ ├── scoringbase.h │ └── transformbase.h └── mputil │ └── simdscan.h ├── libmympbase ├── CMakeLists.txt └── mplayout │ ├── CuMemoryBase.cpp │ └── CuMemoryBase.h ├── libutil ├── CLOptions.cpp ├── CLOptions.h ├── CMakeLists.txt ├── alpha.cpp ├── alpha.h ├── cnsts.h ├── debug.h ├── format.h ├── macros.h ├── mptimer.h ├── msg.cpp ├── msg.h ├── mybase.h ├── mydirent.cpp ├── mydirent.h 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