├── .Rbuildignore ├── DESCRIPTION ├── Dockerfile ├── LICENSE ├── NAMESPACE ├── R ├── AlignmentMatrix.R ├── AllPairwiseAlign.R ├── CLUSTpred.R ├── LTRdigest.R ├── LTRharvest.R ├── LTRpred.R ├── LTRpred.meta.R ├── NW.Align.R ├── ORFpred.R ├── SimMatAbundance.R ├── assign.short.sci.name.R ├── bcolor.R ├── clust2fasta.R ├── cluster.members.R ├── cn2bed.R ├── combinePreds.R ├── customColors.R ├── dfam.query.R ├── file.check.R ├── file.move.R ├── filter.jumpers.R ├── filter.uc.R ├── generate.multi.quality.filter.meta.R ├── genome.summary.R ├── get.pred.filenames.R ├── get.seqs.R ├── gridPlotAssemblyVersions.R ├── join.with.genome.tbl.R.R ├── ltr.cn.R ├── ltr_age_estimation.R ├── meta.apply.R ├── meta.seq.space.R ├── meta.summarize.R ├── motif.count.R ├── pairwise.wilcox.test.R ├── pairwise.z.test.R ├── plotLTRSim.R ├── plot_element_distr_along_chromosome.R ├── pred2GRanges.R ├── pred2bed.R ├── pred2csv.R ├── pred2fasta.R ├── pred2gff.R ├── pred2orfseqs.R ├── pred2tsv.R ├── quality.filter.R ├── quality.filter.meta.R ├── quant.cds.space.R ├── quant.protein.space.R ├── quant.repeat.space.R ├── quant.space.meta.R ├── read.blast6out.R ├── read.dfam.R ├── read.ltrpred.R ├── read.orfs.R ├── read.prediction.R ├── read.seqs.R ├── read.tabout.R ├── read.uc.R ├── rename.fasta.R ├── rename.fasta.meta.R ├── rename.organisms.R ├── repbase.clean.R ├── repbase.filter.R ├── repbase.query.R ├── str_chop_vec.R ├── superfamilyDistr.R ├── test_installation_blast.R ├── test_installation_gt.R ├── test_installation_hmmer.R ├── test_installation_perl.R ├── test_installation_usearch.R ├── test_installation_vsearch.R ├── tidy.datasheet.R ├── totalRepeatSpace.R └── ws.wrap.path.R ├── README.md ├── Sc_LTRpred.pdf ├── Sc_LTRpred.png ├── docs ├── .DS_Store ├── 404.html ├── LICENSE-text.html ├── articles │ ├── Introduction.html │ ├── Introduction_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ └── header-attrs-2.11 │ │ │ └── header-attrs.js │ ├── LTRfeatures.png │ └── index.html ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── inst │ └── LTRpred_logo.png ├── jquery.sticky-kit.min.js ├── link.svg ├── paper.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml └── reference │ ├── AllPairwiseAlign.html │ ├── CLUSTpred.html │ ├── LTRdigest.html │ ├── LTRharvest.html │ ├── LTRpred.html │ ├── LTRpred.meta.html │ ├── ORFpred.html │ ├── Rplot001.png │ ├── SimMatAbundance.html │ ├── assign.short.sci.name.html │ ├── bcolor.html │ ├── check_annotation_ltrpred.html │ ├── chromoMapChromosomeFile.html │ ├── clust2fasta.html │ ├── cluster.members.html │ ├── cn2bed.html │ ├── combinePreds.html │ ├── dfam.query.html │ ├── file.move.html │ ├── filter.jumpers.html │ ├── filter.uc.html │ ├── generate.multi.quality.filter.meta.html │ ├── genome.summary.html │ ├── get.pred.filenames.html │ ├── get.seqs.html │ ├── gridPlotAssemblyVersions.html │ ├── index.html │ ├── join.with.genome.tbl.html │ ├── ltr.cn.html │ ├── ltr_age_estimation.html │ ├── meta.apply.html │ ├── meta.seq.space.html │ ├── meta.summarize.html │ ├── motif.count.html │ ├── output │ ├── output.csv │ ├── plotCN.html │ ├── plotChromoMap.html │ ├── plotCluster.html │ ├── plotDomain-1.png │ ├── plotDomain.html │ ├── plotFamily-1.png │ ├── plotFamily.html │ ├── plotInterSpeciesCluster.html │ ├── plotLTRRange.html │ ├── plotLTRSim.html │ ├── plotLTRSpace.html │ ├── plotMainInterSpeciesCluster.html │ ├── plotProteinSpace.html │ ├── plotRanges.html │ ├── plotRepeatSpace.html │ ├── plotRepeatSpaceCval.html │ ├── plotSimCount.html │ ├── plotSize.html │ ├── plotSizeJumpers.html │ ├── plotSizeMulti.html │ ├── plot_copynumber_individual.html │ ├── plot_copynumber_kingdom.html │ ├── plot_copynumber_species.html │ ├── plot_element_distr_along_chromosome.html │ ├── plot_ltrwidth_individual.html │ ├── plot_ltrwidth_kingdom.html │ ├── plot_ltrwidth_species.html │ ├── plot_pbswidth_kingdom.html │ ├── pred2GRanges.html │ ├── pred2bed.html │ ├── pred2chromoMap.html │ ├── pred2csv.html │ ├── pred2fasta.html │ ├── pred2gff.html │ ├── pred2orfseqs.html │ ├── pred2tsv.html │ ├── quality.filter.html │ ├── quality.filter.meta.html │ ├── quant.cds.space.html │ ├── quant.protein.space.html │ ├── quant.repeat.space.html │ ├── quant.space.meta.html │ ├── read.blast6out.html │ ├── read.dfam.html │ ├── read.ltrpred.html │ ├── read.orfs.html │ ├── read.prediction.html │ ├── read.seqs.html │ ├── read.tabout.html │ ├── read.uc.html │ ├── rename.fasta.html │ ├── rename.fasta.meta.html │ ├── rename.organisms.html │ ├── repbase.clean.html │ ├── repbase.filter.html │ ├── repbase.query.html │ ├── test.gff │ ├── tidy.datasheet.html │ ├── totalRepeatSpace.html │ └── ws.wrap.path.html ├── inst ├── Athaliana_TAIR10_chr_all_LTRpred_DataSheet.csv ├── GenomeMatrix.csv ├── HMMs │ ├── hmm_Gypsy.hmm │ ├── hmm_IN_DBD_C.hmm │ ├── hmm_Integrase_Zn.hmm │ ├── hmm_RNase_H.hmm │ ├── hmm_RVT_1.hmm │ ├── hmm_RVT_2.hmm │ ├── hmm_RdRP_1.hmm │ ├── hmm_RdRP_2.hmm │ ├── hmm_RdRP_3.hmm │ ├── hmm_RdRP_4.hmm │ ├── hmm_TLV_coat.hmm │ ├── hmm_retrotrans_gag.hmm │ └── hmm_rve.hmm ├── Hsapiens_ChrY-ltrdigest_3ltr.fas ├── Hsapiens_ChrY-ltrdigest_5ltr.fas ├── Hsapiens_ChrY.fa ├── Hsapiens_ChrY_LTRpred_DataSheet.tsv ├── LTRpred_logo.png ├── LTRseqs.fas ├── SimMatrix.csv ├── TAIR10_chr_all-ltrdigest_tabout.csv ├── TAIR10_chr_all_LTRdigestPrediction.gff ├── example_dfam.out ├── hg38-tRNAs.fa ├── nt.fa ├── tRNAs │ ├── eukaryotic-tRNAs.fa │ ├── hg38-tRNAs.fa │ ├── plants-tRNA_cat.fa │ ├── sacCer3-tRNAs.fa │ └── tRNA_library.fa ├── test.blast6out └── test.uc ├── man ├── AllPairwiseAlign.Rd ├── CLUSTpred.Rd ├── LTRdigest.Rd ├── LTRharvest.Rd ├── LTRpred.Rd ├── LTRpred.meta.Rd ├── ORFpred.Rd ├── SimMatAbundance.Rd ├── assign.short.sci.name.Rd ├── bcolor.Rd ├── clust2fasta.Rd ├── cluster.members.Rd ├── cn2bed.Rd ├── combinePreds.Rd ├── dfam.query.Rd ├── file.move.Rd ├── filter.jumpers.Rd ├── filter.uc.Rd ├── generate.multi.quality.filter.meta.Rd ├── genome.summary.Rd ├── get.pred.filenames.Rd ├── get.seqs.Rd ├── gridPlotAssemblyVersions.Rd ├── join.with.genome.tbl.Rd ├── ltr.cn.Rd ├── ltr_age_estimation.Rd ├── meta.apply.Rd ├── meta.seq.space.Rd ├── meta.summarize.Rd ├── motif.count.Rd ├── plotLTRSim.Rd ├── plot_element_distr_along_chromosome.Rd ├── pred2GRanges.Rd ├── pred2bed.Rd ├── pred2csv.Rd ├── pred2fasta.Rd ├── pred2gff.Rd ├── pred2orfseqs.Rd ├── pred2tsv.Rd ├── quality.filter.Rd ├── quality.filter.meta.Rd ├── quant.cds.space.Rd ├── quant.protein.space.Rd ├── quant.repeat.space.Rd ├── quant.space.meta.Rd ├── read.blast6out.Rd ├── read.dfam.Rd ├── read.ltrpred.Rd ├── read.orfs.Rd ├── read.prediction.Rd ├── read.seqs.Rd ├── read.tabout.Rd ├── read.uc.Rd ├── rename.fasta.Rd ├── rename.fasta.meta.Rd ├── rename.organisms.Rd ├── repbase.clean.Rd ├── repbase.filter.Rd ├── repbase.query.Rd ├── tidy.datasheet.Rd ├── totalRepeatSpace.Rd └── ws.wrap.path.Rd ├── paper.bib ├── paper.md ├── tests ├── testthat.R └── testthat │ └── test-read.blast6out.R └── 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