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bin/EDTA_processK.pl
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bin/panEDTA.sh
share/EDTA/EDTA.pl
share/EDTA/EDTA_2.2.x.yml
share/EDTA/EDTA_processK.1.pl
share/EDTA/EDTA_processK.pl
share/EDTA/EDTA_raw.pl
share/EDTA/LICENSE
share/EDTA/README.md
share/EDTA/bin/Class_modify_EDTA_intact_gff.py
share/EDTA/bin/Filter_and_format_blast_for_RECON.pl
share/EDTA/bin/RM_summary.pl
share/EDTA/bin/RMout2bed.pl
share/EDTA/bin/TE_Sequence_Ontology.txt
share/EDTA/bin/TE_consistency.py
share/EDTA/bin/TE_purifier.pl
share/EDTA/bin/TE_sankey_plotter.py
share/EDTA/bin/add_id.pl
share/EDTA/bin/bed2gff.pl
share/EDTA/bin/buildSummary.pl
share/EDTA/bin/call_seq_by_list.pl
share/EDTA/bin/classify_by_lib_RM.pl
share/EDTA/bin/clean_GRF_TIR.pl
share/EDTA/bin/cleanup_TE.pl
share/EDTA/bin/cleanup_misclas.pl
share/EDTA/bin/cleanup_nested.pl
share/EDTA/bin/cleanup_nested_mmseq.pl
share/EDTA/bin/cleanup_nested_old.pl
share/EDTA/bin/cleanup_nonTE.pl
share/EDTA/bin/cleanup_proteins.pl
share/EDTA/bin/cleanup_tandem.pl
share/EDTA/bin/cleanup_uniq.pl
share/EDTA/bin/combine_RMrows.pl
share/EDTA/bin/combine_overlap.pl
share/EDTA/bin/count_base.pl
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share/EDTA/bin/count_mask.pl
share/EDTA/bin/count_nested.pl
share/EDTA/bin/count_repeats.pl
share/EDTA/bin/cut.pl
share/EDTA/bin/density_plot.R
share/EDTA/bin/density_table.py
share/EDTA/bin/div_plot2.R
share/EDTA/bin/div_table.pl
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share/EDTA/bin/evaluation.pl
share/EDTA/bin/fffx
share/EDTA/bin/filter_DTT.pl
share/EDTA/bin/filter_and_format_trf_consensus.pl
share/EDTA/bin/filter_copy_number.pl
share/EDTA/bin/filter_gff3.pl
share/EDTA/bin/filter_gff_TIR.pl
share/EDTA/bin/filter_helitronscanner.pl
share/EDTA/bin/find_flTE.pl
share/EDTA/bin/flanking_filter.pl
share/EDTA/bin/format_TElib.pl
share/EDTA/bin/format_gff3.pl
share/EDTA/bin/format_helitronscanner_out.pl
share/EDTA/bin/format_intact_gff3.pl
share/EDTA/bin/get_consistent_TE.pl
share/EDTA/bin/get_ext_seq.pl
share/EDTA/bin/get_frag.pl
share/EDTA/bin/get_interspersed_consensus.pl
share/EDTA/bin/get_lib_len.pl
share/EDTA/bin/get_range.pl
share/EDTA/bin/get_range2.pl
share/EDTA/bin/gff2RMout.pl
share/EDTA/bin/gff2bed.pl
share/EDTA/bin/gff2gtf.pl
share/EDTA/bin/gff_cmb.pl
share/EDTA/bin/keep_nest.pl
share/EDTA/bin/label_solo_LTR.pl
share/EDTA/bin/make_bed_with_intact.pl
share/EDTA/bin/make_gff3.pl
share/EDTA/bin/make_gff3_with_RMout.pl
share/EDTA/bin/make_gff3_with_intact.pl
share/EDTA/bin/make_masked.pl
share/EDTA/bin/make_panTElib.pl
share/EDTA/bin/name_code_decode.pl
share/EDTA/bin/output_by_list.pl
share/EDTA/bin/paf2blast6_chunking2_parallel3_ordered_parts.py
share/EDTA/bin/post-processing.sbatch
share/EDTA/bin/print_hist6.py
share/EDTA/bin/purger.pl
share/EDTA/bin/rename_LTR.pl
share/EDTA/bin/rename_LTR_skim.pl
share/EDTA/bin/rename_RM_TE.pl
share/EDTA/bin/rename_TE.pl
share/EDTA/bin/rename_by_list.pl
share/EDTA/bin/rename_tirlearner.pl
share/EDTA/bin/run_helitron_scanner.py
share/EDTA/bin/run_helitron_scanner.sh
share/EDTA/bin/seqid_codec.pl
share/EDTA/bin/split_overlap.pl
share/EDTA/bin/substract.pl
share/EDTA/bin/substract_parallel.pl
share/EDTA/bin/update_LTRbound.pl
share/EDTA/build_env_setup.sh
share/EDTA/conda_build.sh
share/EDTA/database/HelitronScanner.training.set.fa
share/EDTA/database/README.md
share/EDTA/database/Rice_MSU7.fasta.std7.0.0.out
share/EDTA/database/Tpases020812DNA
share/EDTA/database/Tpases020812LINE
share/EDTA/database/alluniRefprexp082813
share/EDTA/database/athrep.updated.nonredun.fasta
share/EDTA/database/dummy060817.fa
share/EDTA/database/maizeTE02052020
share/EDTA/database/rice7.0.0.liban
share/EDTA/database/rice7.0.0.liban.Helitron
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share/EDTA/development/EDTA workflow.pdf
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share/EDTA/development/EDTA_b2.pl
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share/EDTA/development/EDTA_processB1.pl
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share/EDTA/development/panEDTA.v0.1.sh
share/EDTA/development/patch.pl
share/EDTA/development/patch_1.8.3_to_1.9.0.pl
share/EDTA/lib-test.pl
share/EDTA/metadata_conda_debug.yaml
share/EDTA/panEDTA.sh
share/EDTA/test/Alyrata.test.fa
share/EDTA/test/Col.test.fa
share/EDTA/test/Ler.test.fa
share/EDTA/test/README.txt
share/EDTA/test/genome.cds.fa
share/EDTA/test/genome.cds.list
share/EDTA/test/genome.exclude.bed
share/EDTA/test/genome.fa
