├── .gitmodules ├── README.md ├── bin ├── Combine_for_Two ├── LTR_Boundary_Optimizer.py ├── LTR_detect ├── MSPCollect.pl ├── Matrices │ ├── crossmatch │ │ ├── 14p35g.matrix │ │ ├── 14p37g.matrix │ │ ├── 14p39g.matrix │ │ ├── 14p41g-Hpad.matrix │ │ ├── 14p41g.matrix │ │ ├── 14p43g.matrix │ │ ├── 14p45g.matrix │ │ ├── 14p47g.matrix │ │ ├── 14p49g.matrix │ │ ├── 14p51g.matrix │ │ ├── 14p53g.matrix │ │ ├── 18p35g.matrix │ │ ├── 18p37g.matrix │ │ ├── 18p39g.matrix │ │ ├── 18p41g-Hpad.matrix │ │ ├── 18p41g.matrix │ │ ├── 18p43g.matrix │ │ ├── 18p45g.matrix │ │ ├── 18p47g.matrix │ │ ├── 18p49g.matrix │ │ ├── 18p51g.matrix │ │ ├── 18p53g.matrix │ │ ├── 20p35g.matrix │ │ ├── 20p37g.matrix │ │ ├── 20p39g.matrix │ │ ├── 20p41g-Hpad.matrix │ │ ├── 20p41g.matrix │ │ ├── 20p43g.matrix │ │ ├── 20p45g.matrix │ │ ├── 20p47g.matrix │ │ ├── 20p49g.matrix │ │ ├── 20p51g.matrix │ │ ├── 20p53g.matrix │ │ ├── 25p35g.matrix │ │ ├── 25p37g.matrix │ │ ├── 25p39g.matrix │ │ ├── 25p41g-Hpad.matrix │ │ ├── 25p41g.matrix │ │ ├── 25p43g.matrix │ │ ├── 25p45g.matrix │ │ ├── 25p47g.matrix │ │ ├── 25p49g.matrix │ │ ├── 25p51g.matrix │ │ ├── 25p53g.matrix │ │ ├── 30p43g.matrix │ │ ├── 30p53g.matrix │ │ ├── comparison.matrix │ │ ├── ctools.matrix │ │ ├── insertlinup.matrix │ │ └── linup.matrix │ ├── linupmatrix │ ├── ncbi │ │ └── nt │ │ │ ├── 14p41g-Hpad.matrix │ │ │ ├── 18p41g-Hpad.matrix │ │ │ ├── 20p41g-Hpad.matrix │ │ │ ├── 25p41g-Hpad.matrix │ │ │ ├── at.matrix │ │ │ ├── at.matrix.4.2 │ │ │ ├── at.matrix.4.4 │ │ │ ├── comparison.matrix │ │ │ ├── comparison.matrix.4.2 │ │ │ ├── comparison.matrix.4.4 │ │ │ ├── ctools.matrix │ │ │ ├── ctools.matrix.4.2 │ │ │ ├── ctools.matrix.4.4 │ │ │ ├── edge_extension.matrix │ │ │ ├── edge_extension.matrix.4.2 │ │ │ ├── edge_extension.matrix.4.4 │ │ │ ├── insertlinup.matrix │ │ │ ├── linup.matrix │ │ │ ├── simple.matrix │ │ │ ├── simple.matrix.4.2 │ │ │ ├── simple.matrix.4.4 │ │ │ ├── simple1.matrix │ │ │ ├── simple1.matrix.4.2 │ │ │ ├── simple1.matrix.4.4 │ │ │ ├── symmetricNscores1matrix │ │ │ ├── symmetricNscores1matrix.4.2 │ │ │ └── symmetricNscores1matrix.4.4 │ └── wublast │ │ ├── aa │ │ └── comparison.matrix │ │ └── nt │ │ ├── at.matrix │ │ ├── at.matrix.4.2 │ │ ├── at.matrix.4.4 │ │ ├── comparison.matrix │ │ ├── comparison.matrix.4.2 │ │ ├── comparison.matrix.4.4 │ │ ├── edge_extension.matrix │ │ ├── edge_extension.matrix.4.2 │ │ ├── edge_extension.matrix.4.4 │ │ ├── simple.matrix │ │ ├── simple.matrix.4.2 │ │ ├── simple.matrix.4.4 │ │ ├── simple1.matrix │ │ ├── simple1.matrix.4.2 │ │ └── simple1.matrix.4.4 ├── Pan_TE ├── RECONUtils.pm ├── Refiner.py ├── Refiner │ ├── adaptive_scoring.py │ ├── config.py │ ├── legacy_adapter.py │ ├── main.py │ ├── main_with_legacy.py │ ├── migrate_legacy_phase1.py │ ├── optimized_te_sampling.py │ ├── phase1_screening_optimized.py │ ├── phase2_chimera_splitting.py │ ├── phase2_chimera_splitting_improved.py │ ├── phase3_consensus_building.py │ ├── phase3_stratified_integration.py │ ├── phase4_genome_masking.py │ ├── stratified_biological_filter.py │ ├── te_aware_sampling_strategy.py │ ├── two_stage_sampling.py │ ├── two_stage_sampling_optimized.py │ └── utils │ │ ├── __pycache__ │ │ ├── alignment_utils.cpython-38.pyc │ │ ├── cache_utils.cpython-38.pyc │ │ ├── complexity_utils.cpython-38.pyc │ │ ├── fast_sequence_extractor.cpython-38.pyc │ │ ├── genome_renamer.cpython-38.pyc │ │ ├── id_mapper.cpython-38.pyc │ │ ├── repeatmasker_parser.cpython-38.pyc │ │ ├── robust_runner.cpython-38.pyc │ │ ├── safe_sequence_extractor.cpython-38.pyc │ │ └── sequence_utils.cpython-38.pyc │ │ ├── alignment_utils.py │ │ ├── blast_utils.py │ │ ├── cache_utils.py │ │ ├── complexity_utils.py │ │ ├── fast_sequence_extractor.py │ │ ├── genome_renamer.py │ │ ├── id_format_checker.py │ │ ├── id_mapper.py │ │ ├── repeatmasker_parser.py │ │ ├── robust_runner.py │ │ ├── safe_sequence_extractor.py │ │ └── sequence_utils.py ├── Refiner_for_Graph ├── TE_Merge ├── TE_Merge_improved ├── build_RS ├── build_for_RECON ├── build_ltr_consensus.py ├── clean_seq ├── clean_seq_fast ├── decode_gfa.pl ├── index ├── ltr_modules │ ├── LTR_BoundaryRefiner.py │ ├── LTR_ChimeraDetector.py │ ├── LTR_ConsensusBuilder.py │ ├── LTR_QualityValidator.py │ ├── USAGE_EXAMPLES.md │ ├── __init__.py │ ├── __pycache__ │ │ ├── LTR_BoundaryRefiner.cpython-38.pyc │ │ ├── LTR_ChimeraDetector.cpython-38.pyc │ │ ├── LTR_ConsensusBuilder.cpython-38.pyc │ │ ├── LTR_QualityValidator.cpython-38.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── genome_utils.cpython-38.pyc │ │ └── shared_utils.cpython-38.pyc │ ├── genome_utils.py │ └── shared_utils.py ├── process_for_classify.py ├── recon_checkpoint_manager ├── renameTE ├── run_Classifier ├── run_RECON_advanced ├── run_RECON_sampling_independent.pl └── vcf_processor.py ├── env └── pgta.yml ├── lib └── RECON │ ├── Config.pm │ ├── Core.pm │ ├── Logger.pm │ ├── MaskedTrack.pm │ ├── SamplingTrack.pm │ └── Utils.pm ├── share ├── .DS_Store ├── ArrayList.pm ├── ArrayListIterator.pm ├── CrossmatchSearchEngine.pm ├── DFAM.pm ├── DFAMRecord.pm ├── DupMasker ├── EMBL.pm ├── FastaDB.pm ├── HMMERSearchEngine.pm ├── HTMLAnnotHeader.html ├── Job.pm ├── LibraryUtils.pm ├── Matrix.pm ├── MultAln.pm ├── NCBIBlastSearchEngine.pm ├── NCBIBlastXSearchEngine.pm ├── NeedlemanWunschGotohAlgorithm.pm ├── PRSearchResult.pm ├── ProcessRepeats ├── PubRef.pm ├── README.md ├── ReleaseNotes ├── RepModelConfig.pm ├── RepbaseEMBL.pm ├── RepbaseRecord.pm ├── RepeatMasker ├── RepeatMaskerConfig.pm ├── RepeatMaskerConfig.pm.bak ├── RepeatProteinMask ├── RepeatRecord.pm ├── RepeatUtil.pm ├── SearchEngineI.pm ├── SearchResult.pm ├── SearchResultCollection.pm ├── SeedAlignment.pm ├── SeedAlignmentCollection.pm ├── SeqDBI.pm ├── SequenceSimilarityMatrix.pm ├── SimpleBatcher.pm ├── TRF.pm ├── TRFResult.pm ├── TRFSearchResult.pm ├── Task.pm ├── Taxonomy.pm ├── ThreadedJob.pm ├── ThreadedTaskSimple.pm ├── WUBlastSearchEngine.pm ├── WUBlastXSearchEngine.pm ├── addRepBase.pl ├── bluegrad.jpg ├── build_env_setup.sh ├── conda_build.sh ├── configure ├── daterepeats.help ├── famdb.py ├── metadata_conda_debug.yaml └── repeatmasker.help └── submodule └── ClassifyTE ├── .gitignore ├── CLAUDE.md ├── CV_train.py ├── HierStack ├── __init__.py ├── classification.py ├── hierarchy.py ├── lcpnb.py ├── model.py ├── nllcpn.py └── stackingClassifier.py ├── LICENSE.md ├── ReadMe.md ├── benchmark_parallel.py ├── environment.yml ├── evaluate.py ├── features ├── .txt ├── BufferReaderAndWriter.class ├── BufferReaderAndWriter.java ├── KmersFeaturesCollector.class ├── KmersFeaturesCollector.java ├── ParallelKmersFeaturesCollector.class ├── ParallelKmersFeaturesCollector.java ├── getFileNameAndHeader.py ├── kanalyze-2.0.0 │ └── code │ │ ├── COPYING.LESSER.txt │ │ ├── COPYING.txt │ │ ├── KAnalyzeManual.pdf │ │ ├── README.txt │ │ ├── ReleaseNotes.txt │ │ ├── cite.exe │ │ ├── commons-lang3-3.4.jar │ │ ├── count.exe │ │ ├── count.kc │ │ ├── java-getopt-1.0.14.jar │ │ ├── kanalyze.jar │ │ ├── list.txt │ │ 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