├── .github └── ISSUE_TEMPLATE │ ├── bug_report.md │ └── question.md ├── BuildDatabase ├── Job.pm ├── LICENSE ├── LTRPipeline ├── Libraries ├── at.lib └── simple.lib ├── 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 ├── MultAln.pm ├── NeedlemanWunschGotohAlgorithm.pm ├── README.md ├── RELEASE-NOTES ├── Refiner ├── RepModelConfig.pm ├── RepeatClassifier ├── RepeatModeler ├── RepeatUtil.pm ├── SeedAlignment.pm ├── SeedAlignmentCollection.pm ├── SequenceSimilarityMatrix.pm ├── TRFMask ├── Task.pm ├── ThreadedJob.pm ├── ThreadedTaskSimple.pm ├── configure └── util ├── AutoRunBlocker.pl ├── Blocker.pl ├── ClusterPartialMatchingSubs.pl ├── CntSubst ├── Linup ├── TSD.pl ├── align.pl ├── alignAndCallConsensus.pl ├── bestwindow.pl ├── extendFlankingSeqs.pl ├── fasta-trf-filter.pl ├── generateSeedAlignments.pl ├── javascript ├── isb │ ├── .swp │ ├── AlignmentSummary-201311.js │ ├── AlignmentSummary.js │ └── AlignmentViewer.js └── zynga-1.2.2-10 │ ├── Animate.js │ └── Scroller.js ├── renameIds.pl ├── resolveIndels.pl ├── rmblast.pl ├── viewMSA.pl └── visualizeAlignPNG.pl /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Dfam-consortium/RepeatModeler/HEAD/.github/ISSUE_TEMPLATE/bug_report.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/question.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Dfam-consortium/RepeatModeler/HEAD/.github/ISSUE_TEMPLATE/question.md -------------------------------------------------------------------------------- /BuildDatabase: -------------------------------------------------------------------------------- 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