bin/.repeatmasker-post-link.sh
bin/DupMasker
bin/ProcessRepeats
bin/RM2Bed.py
bin/RepeatMasker
bin/RepeatProteinMask
bin/bigRmskAlignBed.as
bin/bigRmskBed.as
bin/buildRMLibFromEMBL.pl
bin/buildSummary.pl
bin/calcDivergenceFromAlign.pl
bin/combineRMFiles.pl
bin/createRepeatLandscape.pl
bin/dupliconToSVG.pl
bin/getRepeatMaskerBatch.pl
bin/maskFile.pl
bin/renumberRMFiles.pl
bin/rmOut2Fasta.pl
bin/rmOutToGFF3.pl
bin/rmToTrackHub.pl
bin/rmToUCSCTables.pl
bin/trfMask
bin/wublastToCrossmatch.pl
share/RepeatMasker/ArrayList.pm
share/RepeatMasker/ArrayListIterator.pm
share/RepeatMasker/CrossmatchSearchEngine.pm
share/RepeatMasker/DFAM.pm
share/RepeatMasker/DFAMRecord.pm
share/RepeatMasker/DupMasker
share/RepeatMasker/EMBL.pm
share/RepeatMasker/FastaDB.pm
share/RepeatMasker/HMMERSearchEngine.pm
share/RepeatMasker/HTMLAnnotHeader.html
share/RepeatMasker/INSTALL
share/RepeatMasker/LICENSE
share/RepeatMasker/Libraries/Artefacts.embl
share/RepeatMasker/Libraries/Dfam.h5
share/RepeatMasker/Libraries/README.meta
share/RepeatMasker/Libraries/RMRBMeta.embl
share/RepeatMasker/Libraries/RepeatAnnotationData.pm
share/RepeatMasker/Libraries/RepeatMasker.lib
share/RepeatMasker/Libraries/RepeatMasker.lib.ndb
share/RepeatMasker/Libraries/RepeatMasker.lib.nhr
share/RepeatMasker/Libraries/RepeatMasker.lib.nin
share/RepeatMasker/Libraries/RepeatMasker.lib.njs
share/RepeatMasker/Libraries/RepeatMasker.lib.not
share/RepeatMasker/Libraries/RepeatMasker.lib.nsq
share/RepeatMasker/Libraries/RepeatMasker.lib.ntf
share/RepeatMasker/Libraries/RepeatMasker.lib.nto
share/RepeatMasker/Libraries/RepeatMaskerLib.h5
share/RepeatMasker/Libraries/RepeatPeps.lib
share/RepeatMasker/Libraries/RepeatPeps.lib.pdb
share/RepeatMasker/Libraries/RepeatPeps.lib.phr
share/RepeatMasker/Libraries/RepeatPeps.lib.pin
share/RepeatMasker/Libraries/RepeatPeps.lib.pjs
share/RepeatMasker/Libraries/RepeatPeps.lib.pot
share/RepeatMasker/Libraries/RepeatPeps.lib.psq
share/RepeatMasker/Libraries/RepeatPeps.lib.ptf
share/RepeatMasker/Libraries/RepeatPeps.lib.pto
share/RepeatMasker/Libraries/RepeatPeps.readme
share/RepeatMasker/Libraries/taxonomy.dat
share/RepeatMasker/LibraryUtils.pm
share/RepeatMasker/Matrices/crossmatch/14p35g.matrix
share/RepeatMasker/Matrices/crossmatch/14p37g.matrix
share/RepeatMasker/Matrices/crossmatch/14p39g.matrix
share/RepeatMasker/Matrices/crossmatch/14p41g.matrix
share/RepeatMasker/Matrices/crossmatch/14p43g.matrix
share/RepeatMasker/Matrices/crossmatch/14p45g.matrix
share/RepeatMasker/Matrices/crossmatch/14p47g.matrix
share/RepeatMasker/Matrices/crossmatch/14p49g.matrix
share/RepeatMasker/Matrices/crossmatch/14p51g.matrix
share/RepeatMasker/Matrices/crossmatch/14p53g.matrix
share/RepeatMasker/Matrices/crossmatch/18p35g.matrix
share/RepeatMasker/Matrices/crossmatch/18p37g.matrix
share/RepeatMasker/Matrices/crossmatch/18p39g.matrix
share/RepeatMasker/Matrices/crossmatch/18p41g.matrix
share/RepeatMasker/Matrices/crossmatch/18p43g.matrix
share/RepeatMasker/Matrices/crossmatch/18p45g.matrix
share/RepeatMasker/Matrices/crossmatch/18p47g.matrix
share/RepeatMasker/Matrices/crossmatch/18p49g.matrix
share/RepeatMasker/Matrices/crossmatch/18p51g.matrix
share/RepeatMasker/Matrices/crossmatch/18p53g.matrix
share/RepeatMasker/Matrices/crossmatch/20p35g.matrix
share/RepeatMasker/Matrices/crossmatch/20p37g.matrix
share/RepeatMasker/Matrices/crossmatch/20p39g.matrix
share/RepeatMasker/Matrices/crossmatch/20p41g.matrix
share/RepeatMasker/Matrices/crossmatch/20p43g.matrix
share/RepeatMasker/Matrices/crossmatch/20p45g.matrix
share/RepeatMasker/Matrices/crossmatch/20p47g.matrix
share/RepeatMasker/Matrices/crossmatch/20p49g.matrix
share/RepeatMasker/Matrices/crossmatch/20p51g.matrix
share/RepeatMasker/Matrices/crossmatch/20p53g.matrix
share/RepeatMasker/Matrices/crossmatch/25p35g.matrix
share/RepeatMasker/Matrices/crossmatch/25p37g.matrix
share/RepeatMasker/Matrices/crossmatch/25p39g.matrix
share/RepeatMasker/Matrices/crossmatch/25p41g.matrix
share/RepeatMasker/Matrices/crossmatch/25p43g.matrix
share/RepeatMasker/Matrices/crossmatch/25p45g.matrix
share/RepeatMasker/Matrices/crossmatch/25p47g.matrix
share/RepeatMasker/Matrices/crossmatch/25p49g.matrix
share/RepeatMasker/Matrices/crossmatch/25p51g.matrix
share/RepeatMasker/Matrices/crossmatch/25p53g.matrix
share/RepeatMasker/Matrices/crossmatch/30p53g.matrix
share/RepeatMasker/Matrices/crossmatch/at.matrix
share/RepeatMasker/Matrices/crossmatch/identity.matrix
share/RepeatMasker/Matrices/crossmatch/simple.matrix
share/RepeatMasker/Matrices/crossmatch/simple1.matrix
share/RepeatMasker/Matrices/crossmatch/transp.matrix
share/RepeatMasker/Matrices/ncbi/nt/14p35g.matrix
share/RepeatMasker/Matrices/ncbi/nt/14p37g.matrix
share/RepeatMasker/Matrices/ncbi/nt/14p39g.matrix
share/RepeatMasker/Matrices/ncbi/nt/14p41g.matrix
share/RepeatMasker/Matrices/ncbi/nt/14p43g.matrix
share/RepeatMasker/Matrices/ncbi/nt/14p45g.matrix
share/RepeatMasker/Matrices/ncbi/nt/14p47g.matrix
share/RepeatMasker/Matrices/ncbi/nt/14p49g.matrix
share/RepeatMasker/Matrices/ncbi/nt/14p51g.matrix
share/RepeatMasker/Matrices/ncbi/nt/14p53g.matrix
share/RepeatMasker/Matrices/ncbi/nt/18p35g.matrix
share/RepeatMasker/Matrices/ncbi/nt/18p37g.matrix
share/RepeatMasker/Matrices/ncbi/nt/18p39g.matrix
share/RepeatMasker/Matrices/ncbi/nt/18p41g.matrix
share/RepeatMasker/Matrices/ncbi/nt/18p43g.matrix
share/RepeatMasker/Matrices/ncbi/nt/18p45g.matrix
share/RepeatMasker/Matrices/ncbi/nt/18p47g.matrix
share/RepeatMasker/Matrices/ncbi/nt/18p49g.matrix
share/RepeatMasker/Matrices/ncbi/nt/18p51g.matrix
share/RepeatMasker/Matrices/ncbi/nt/18p53g.matrix
share/RepeatMasker/Matrices/ncbi/nt/20p35g.matrix
share/RepeatMasker/Matrices/ncbi/nt/20p37g.matrix
share/RepeatMasker/Matrices/ncbi/nt/20p39g.matrix
share/RepeatMasker/Matrices/ncbi/nt/20p41g.matrix
share/RepeatMasker/Matrices/ncbi/nt/20p43g.matrix
share/RepeatMasker/Matrices/ncbi/nt/20p45g.matrix
share/RepeatMasker/Matrices/ncbi/nt/20p47g.matrix
share/RepeatMasker/Matrices/ncbi/nt/20p49g.matrix
share/RepeatMasker/Matrices/ncbi/nt/20p51g.matrix
share/RepeatMasker/Matrices/ncbi/nt/20p53g.matrix
share/RepeatMasker/Matrices/ncbi/nt/25p35g.matrix
share/RepeatMasker/Matrices/ncbi/nt/25p37g.matrix
share/RepeatMasker/Matrices/ncbi/nt/25p39g.matrix
share/RepeatMasker/Matrices/ncbi/nt/25p41g.matrix
share/RepeatMasker/Matrices/ncbi/nt/25p43g.matrix
share/RepeatMasker/Matrices/ncbi/nt/25p45g.matrix
share/RepeatMasker/Matrices/ncbi/nt/25p47g.matrix
share/RepeatMasker/Matrices/ncbi/nt/25p49g.matrix
share/RepeatMasker/Matrices/ncbi/nt/25p51g.matrix
share/RepeatMasker/Matrices/ncbi/nt/25p53g.matrix
share/RepeatMasker/Matrices/ncbi/nt/30p53g.matrix
share/RepeatMasker/Matrices/ncbi/nt/at.matrix
share/RepeatMasker/Matrices/ncbi/nt/atx.matrix
share/RepeatMasker/Matrices/ncbi/nt/identity.matrix
share/RepeatMasker/Matrices/ncbi/nt/ncbiblastdefault.matrix
share/RepeatMasker/Matrices/ncbi/nt/simple.matrix
share/RepeatMasker/Matrices/ncbi/nt/simple1.matrix
share/RepeatMasker/Matrices/ncbi/nt/simplex.matrix
share/RepeatMasker/Matrices/ncbi/nt/wublastdefault.matrix
share/RepeatMasker/Matrices/wublast/aa/14p35g.matrix
share/RepeatMasker/Matrices/wublast/aa/14p37g.matrix
share/RepeatMasker/Matrices/wublast/aa/14p39g.matrix
share/RepeatMasker/Matrices/wublast/aa/14p41g.matrix
share/RepeatMasker/Matrices/wublast/aa/14p43g.matrix
share/RepeatMasker/Matrices/wublast/aa/14p45g.matrix
share/RepeatMasker/Matrices/wublast/aa/14p47g.matrix
share/RepeatMasker/Matrices/wublast/aa/14p49g.matrix
share/RepeatMasker/Matrices/wublast/aa/14p51g.matrix
share/RepeatMasker/Matrices/wublast/aa/14p53g.matrix
share/RepeatMasker/Matrices/wublast/aa/18p35g.matrix
share/RepeatMasker/Matrices/wublast/aa/18p37g.matrix
share/RepeatMasker/Matrices/wublast/aa/18p39g.matrix
share/RepeatMasker/Matrices/wublast/aa/18p41g.matrix
share/RepeatMasker/Matrices/wublast/aa/18p43g.matrix
share/RepeatMasker/Matrices/wublast/aa/18p45g.matrix
share/RepeatMasker/Matrices/wublast/aa/18p47g.matrix
share/RepeatMasker/Matrices/wublast/aa/18p49g.matrix
share/RepeatMasker/Matrices/wublast/aa/18p51g.matrix
share/RepeatMasker/Matrices/wublast/aa/18p53g.matrix
share/RepeatMasker/Matrices/wublast/aa/20p35g.matrix
share/RepeatMasker/Matrices/wublast/aa/20p37g.matrix
share/RepeatMasker/Matrices/wublast/aa/20p39g.matrix
share/RepeatMasker/Matrices/wublast/aa/20p41g.matrix
share/RepeatMasker/Matrices/wublast/aa/20p43g.matrix
share/RepeatMasker/Matrices/wublast/aa/20p45g.matrix
share/RepeatMasker/Matrices/wublast/aa/20p47g.matrix
share/RepeatMasker/Matrices/wublast/aa/20p49g.matrix
share/RepeatMasker/Matrices/wublast/aa/20p51g.matrix
share/RepeatMasker/Matrices/wublast/aa/20p53g.matrix
share/RepeatMasker/Matrices/wublast/aa/25p35g.matrix
share/RepeatMasker/Matrices/wublast/aa/25p37g.matrix
share/RepeatMasker/Matrices/wublast/aa/25p39g.matrix
share/RepeatMasker/Matrices/wublast/aa/25p41g.matrix
share/RepeatMasker/Matrices/wublast/aa/25p43g.matrix
share/RepeatMasker/Matrices/wublast/aa/25p45g.matrix
share/RepeatMasker/Matrices/wublast/aa/25p47g.matrix
share/RepeatMasker/Matrices/wublast/aa/25p49g.matrix
share/RepeatMasker/Matrices/wublast/aa/25p51g.matrix
share/RepeatMasker/Matrices/wublast/aa/25p53g.matrix
share/RepeatMasker/Matrices/wublast/aa/30p53g.matrix
share/RepeatMasker/Matrices/wublast/aa/at.matrix
share/RepeatMasker/Matrices/wublast/aa/identity.matrix
share/RepeatMasker/Matrices/wublast/aa/simple.matrix
share/RepeatMasker/Matrices/wublast/aa/simple1.matrix
share/RepeatMasker/Matrices/wublast/nt/14p35g.matrix
share/RepeatMasker/Matrices/wublast/nt/14p35g.matrix.4.2
share/RepeatMasker/Matrices/wublast/nt/14p35g.matrix.4.4
share/RepeatMasker/Matrices/wublast/nt/20p41g.matrix
share/RepeatMasker/Matrices/wublast/nt/20p41g.matrix.4.2
share/RepeatMasker/Matrices/wublast/nt/20p41g.matrix.4.4
share/RepeatMasker/Matrix.pm
share/RepeatMasker/NCBIBlastSearchEngine.pm
share/RepeatMasker/NCBIBlastXSearchEngine.pm
share/RepeatMasker/PRSearchResult.pm
share/RepeatMasker/ProcessRepeats
share/RepeatMasker/PubRef.pm
share/RepeatMasker/README.md
share/RepeatMasker/ReleaseNotes
share/RepeatMasker/RepbaseEMBL.pm
share/RepeatMasker/RepbaseRecord.pm
share/RepeatMasker/RepeatMasker
share/RepeatMasker/RepeatMaskerConfig.pm
share/RepeatMasker/RepeatMaskerConfig.pm.bak
share/RepeatMasker/RepeatProteinMask
share/RepeatMasker/RepeatRecord.pm
share/RepeatMasker/SearchEngineI.pm
share/RepeatMasker/SearchResult.pm
share/RepeatMasker/SearchResultCollection.pm
share/RepeatMasker/SeqDBI.pm
share/RepeatMasker/SimpleBatcher.pm
share/RepeatMasker/TRF.pm
share/RepeatMasker/TRFResult.pm
share/RepeatMasker/TRFSearchResult.pm
share/RepeatMasker/Taxonomy.pm
share/RepeatMasker/WUBlastSearchEngine.pm
share/RepeatMasker/WUBlastXSearchEngine.pm
share/RepeatMasker/addRepBase.pl
share/RepeatMasker/bluegrad.jpg
share/RepeatMasker/build_env_setup.sh
share/RepeatMasker/conda_build.sh
share/RepeatMasker/configure
share/RepeatMasker/daterepeats.help
share/RepeatMasker/famdb.py
share/RepeatMasker/metadata_conda_debug.yaml
share/RepeatMasker/repeatmasker.help
share/RepeatMasker/util/RM2Bed.py
share/RepeatMasker/util/bigRmskAlignBed.as
share/RepeatMasker/util/bigRmskBed.as
share/RepeatMasker/util/buildRMLibFromEMBL.pl
share/RepeatMasker/util/buildSummary.pl
share/RepeatMasker/util/calcDivergenceFromAlign.pl
share/RepeatMasker/util/combineRMFiles.pl
share/RepeatMasker/util/createRepeatLandscape.pl
share/RepeatMasker/util/dupliconToSVG.pl
share/RepeatMasker/util/getRepeatMaskerBatch.pl
share/RepeatMasker/util/maskFile.pl
share/RepeatMasker/util/renumberRMFiles.pl
share/RepeatMasker/util/rmOut2Fasta.pl
share/RepeatMasker/util/rmOutToGFF3.pl
share/RepeatMasker/util/rmToTrackHub.pl
share/RepeatMasker/util/rmToUCSCTables.pl
share/RepeatMasker/util/trfMask
share/RepeatMasker/util/wublastToCrossmatch.pl