├── README.md ├── assembly └── 01.transcriptBlat2genome │ ├── 01.blat.pl.sh │ ├── 02.stats.pl │ ├── 02.stats.pl.sh │ └── Leaf.trinity.len.stats └── evolution ├── 00.readme.md ├── 01.orthomcl ├── 01.input.pl ├── 01.input.pl.sh ├── 02.runOrthomcl.sh ├── 03.OrthoTypeHistgram.pl ├── 04.OrthoTypeVeen.pl ├── 05.GF.count.pl ├── 3.orthomcl.out.pl ├── compliantFasta.genenum.txt ├── inputseq.txt ├── mysql.setting.template ├── orthomcl.config.template └── poorProteins.fasta ├── 02.phylogenetic ├── 1.splitSeq.pl ├── 2.align.pl ├── 3.connect.pl ├── 4.4Dsites.pl ├── time │ ├── 00.readme.txt │ ├── Nexus2realtime.pl │ ├── Nexus2realtime.pl~ │ ├── baseml.ctl │ ├── in.BV │ ├── mcmctree.2.ctl │ ├── mcmctree.3.ctl │ ├── mlb │ ├── out.BV │ ├── r01 │ │ ├── FigTree.tre │ │ ├── SeedUsed │ │ ├── in.BV │ │ ├── mcmc.txt │ │ ├── mcmctree.2.ctl │ │ └── out_usedata2 │ ├── r02 │ │ ├── FigTree.tre │ │ ├── SeedUsed │ │ ├── in.BV │ │ ├── mcmc.txt │ │ ├── mcmctree.2.ctl │ │ └── out_usedata2 │ ├── species.tree0 │ └── species.tree1 └── tree │ ├── 01.fixname.pl │ ├── 02.replacename.pl │ └── build-tree.pl ├── 03.paml ├── 01.splitSeq.pl ├── 02.prank.pl ├── 03.gblock.pl ├── 04.prepare.paml.Creat.TREE.pl ├── 05.prepare.paml.Creat.CTL.pl ├── 06.paml.pl ├── ctl │ ├── branch-site.Omu.fix.ctl │ ├── branch-site.Omu.nofix.ctl │ ├── branch-site.Ore.fix.ctl │ ├── branch-site.Ore.nofix.ctl │ ├── branch.freeratio.ctl │ ├── branch.oneratio.ctl │ ├── branch.tworatio.Omu.ctl │ ├── branch.tworatio.Ore.ctl │ └── ctl.template ├── scripts │ └── Gblocks2Paml.pl ├── statistics │ ├── 01.freeratio │ │ ├── 01.get.freeratio.diff.tree.pl │ │ ├── 01.get.freeratio.diff.tree.pl~ │ │ ├── 01.get.freeratio.result.pl │ │ ├── 02.rand.plot.pl │ │ ├── 02.rand.plot.pl.R │ │ ├── 02.rand.plot.pl.rand.150genes.10000times.out │ │ ├── 02.rand.plot.pl.rand.150genes.10000times.out.pdf │ │ └── All.freeratio.result.out │ ├── 02.branch │ │ ├── 01.get.branch.result.pl │ │ ├── 02.chi2.pl │ │ ├── 03.fdr.pl │ │ ├── All.branch.chi2.fdr.out │ │ ├── All.branch.chi2.fdr.out.R │ │ ├── All.branch.chi2.out │ │ └── All.branch.out │ └── 03.branch-site │ │ ├── 01.get.brachsite.result.pl │ │ ├── 02.chi2.pl │ │ ├── 03.fdr.pl │ │ ├── All.branchsite.result.chi2.out │ │ ├── All.branchsite.result.out │ │ └── All.freeratio.result.out └── tree │ ├── tree.Omu │ ├── tree.Ore │ └── tree.raw ├── 04.GF_expansion_contruction ├── 00.readme.txt ├── cafetutorial_clade_and_size_filter.py ├── cafetutorial_mcl2rawcafe.py ├── cafetutorial_run1.sh └── cafetutorial_run2.sh ├── 05.psmc ├── 01.psmc.pl ├── 1.bt.psmc.plot.pl ├── epstopdf.pl ├── psmc_plot.g3.pl └── psmc_plot.g3.pl.sh ├── 06.ltr.insert.time ├── 01.split.fasta.pl ├── 02.LTR_finder.pl ├── 02.LTR_finder.pl.sh ├── 03.get.seq.pl ├── 04.classifer.pl ├── 04.classifer.pl.sh ├── 05.align.3.5.soloLTR.pl ├── 05.align.3.5.soloLTR.pl.sh ├── 06.merge.distmat.result.pl ├── 06.merge.distmat.result.pl.out ├── LTR_finder.batch.result │ ├── scaffold10278 │ │ ├── gff │ │ │ ├── scaffold10278_def_lf_summary_seq.txt │ │ │ ├── scaffold10278_def_lf_summary_short.txt │ │ │ ├── scaffold10278_def_ltr_finder.gff │ │ │ ├── scaffold10278_p_20_lf_summary_seq.txt │ │ │ ├── scaffold10278_p_20_lf_summary_short.txt │ │ │ ├── scaffold10278_p_20_ltr_finder.gff │ │ │ ├── scaffold10278_p_30_lf_summary_seq.txt │ │ │ ├── scaffold10278_p_30_lf_summary_short.txt │ │ │ └── scaffold10278_p_30_ltr_finder.gff │ │ └── ltr_finder │ │ │ ├── scaffold10278_LTRFinder_def1_LTR_retrotransposon.fasta │ │ │ ├── scaffold10278_LTRFinder_def1_RR_tract.fasta │ │ │ ├── scaffold10278_LTRFinder_def1_five_prime_LTR.fasta │ │ │ ├── scaffold10278_LTRFinder_def1_primer_binding_site.fasta │ │ │ ├── scaffold10278_LTRFinder_def1_three_prime_LTR.fasta │ │ │ ├── scaffold10278_LTRFinder_def2_LTR_retrotransposon.fasta │ │ │ ├── scaffold10278_LTRFinder_def2_RR_tract.fasta │ │ │ ├── scaffold10278_LTRFinder_def2_five_prime_LTR.fasta │ │ │ ├── scaffold10278_LTRFinder_def2_primer_binding_site.fasta │ │ │ ├── scaffold10278_LTRFinder_def2_three_prime_LTR.fasta │ │ │ ├── scaffold10278_LTRFinder_p_201_LTR_retrotransposon.fasta │ │ │ ├── scaffold10278_LTRFinder_p_201_RR_tract.fasta │ │ │ ├── scaffold10278_LTRFinder_p_201_five_prime_LTR.fasta │ │ │ ├── scaffold10278_LTRFinder_p_201_primer_binding_site.fasta │ │ │ ├── scaffold10278_LTRFinder_p_201_three_prime_LTR.fasta │ │ │ ├── scaffold10278_LTRFinder_p_202_LTR_retrotransposon.fasta │ │ │ ├── scaffold10278_LTRFinder_p_202_RR_tract.fasta │ │ │ ├── scaffold10278_LTRFinder_p_202_five_prime_LTR.fasta │ │ │ ├── scaffold10278_LTRFinder_p_202_primer_binding_site.fasta │ │ │ ├── scaffold10278_LTRFinder_p_202_three_prime_LTR.fasta │ │ │ ├── scaffold10278_LTRFinder_p_301_LTR_retrotransposon.fasta │ │ │ ├── scaffold10278_LTRFinder_p_301_RR_tract.fasta │ │ │ ├── scaffold10278_LTRFinder_p_301_five_prime_LTR.fasta │ │ │ ├── scaffold10278_LTRFinder_p_301_primer_binding_site.fasta │ │ │ ├── scaffold10278_LTRFinder_p_301_three_prime_LTR.fasta │ │ │ ├── scaffold10278_LTRFinder_p_302_LTR_retrotransposon.fasta │ │ │ ├── scaffold10278_LTRFinder_p_302_RR_tract.fasta │ │ │ ├── scaffold10278_LTRFinder_p_302_five_prime_LTR.fasta │ │ │ ├── scaffold10278_LTRFinder_p_302_primer_binding_site.fasta │ │ │ ├── scaffold10278_LTRFinder_p_302_three_prime_LTR.fasta │ │ │ ├── scaffold10278_def_ltr_finder.txt │ │ │ ├── scaffold10278_p_20_ltr_finder.txt │ │ │ └── scaffold10278_p_30_ltr_finder.txt │ └── scaffold10747 │ │ ├── gff │ │ ├── scaffold10747_def_lf_summary_seq.txt │ │ ├── scaffold10747_def_lf_summary_short.txt │ │ ├── scaffold10747_def_ltr_finder.gff │ │ ├── scaffold10747_p_20_lf_summary_seq.txt │ │ ├── scaffold10747_p_20_lf_summary_short.txt │ │ ├── scaffold10747_p_20_ltr_finder.gff │ │ ├── scaffold10747_p_30_lf_summary_seq.txt │ │ ├── scaffold10747_p_30_lf_summary_short.txt │ │ └── scaffold10747_p_30_ltr_finder.gff │ │ └── ltr_finder │ │ ├── scaffold10747_LTRFinder_def1_LTR_retrotransposon.fasta │ │ ├── scaffold10747_LTRFinder_def1_RR_tract.fasta │ │ ├── scaffold10747_LTRFinder_def1_five_prime_LTR.fasta │ │ ├── scaffold10747_LTRFinder_def1_in_core_orf.fasta │ │ ├── scaffold10747_LTRFinder_def1_primer_binding_site.fasta │ │ ├── scaffold10747_LTRFinder_def1_target_site_duplication.fasta │ │ ├── scaffold10747_LTRFinder_def1_three_prime_LTR.fasta │ │ ├── scaffold10747_LTRFinder_p_201_LTR_retrotransposon.fasta │ │ ├── scaffold10747_LTRFinder_p_201_RR_tract.fasta │ │ ├── scaffold10747_LTRFinder_p_201_five_prime_LTR.fasta │ │ ├── scaffold10747_LTRFinder_p_201_in_core_orf.fasta │ │ ├── scaffold10747_LTRFinder_p_201_primer_binding_site.fasta │ │ ├── scaffold10747_LTRFinder_p_201_target_site_duplication.fasta │ │ ├── scaffold10747_LTRFinder_p_201_three_prime_LTR.fasta │ │ ├── scaffold10747_def_ltr_finder.txt │ │ ├── scaffold10747_p_20_ltr_finder.txt │ │ └── scaffold10747_p_30_ltr_finder.txt ├── align_soloLTRs │ ├── scaffold10278_LTRFinder_def1 │ │ ├── scaffold10278_LTRFinder_def1.3.5.ltr.fa │ │ ├── scaffold10278_LTRFinder_def1.3.5.ltr.fa.align │ │ ├── scaffold10278_LTRFinder_def1.3.5.ltr.fa.align.dnadist │ │ ├── scaffold10278_LTRFinder_def1.3.5.ltr.fa.align.phy │ │ └── scaffold10278_LTRFinder_def1.3.5.ltr.fa.align.phylip │ ├── scaffold10278_LTRFinder_def2 │ │ ├── scaffold10278_LTRFinder_def2.3.5.ltr.fa │ │ ├── scaffold10278_LTRFinder_def2.3.5.ltr.fa.align │ │ ├── scaffold10278_LTRFinder_def2.3.5.ltr.fa.align.dnadist │ │ ├── scaffold10278_LTRFinder_def2.3.5.ltr.fa.align.phy │ │ └── scaffold10278_LTRFinder_def2.3.5.ltr.fa.align.phylip │ └── scaffold10747_LTRFinder_def1 │ │ ├── scaffold10747_LTRFinder_def1.3.5.ltr.fa │ │ ├── scaffold10747_LTRFinder_def1.3.5.ltr.fa.align │ │ ├── scaffold10747_LTRFinder_def1.3.5.ltr.fa.align.dnadist │ │ ├── scaffold10747_LTRFinder_def1.3.5.ltr.fa.align.phy │ │ └── scaffold10747_LTRFinder_def1.3.5.ltr.fa.align.phylip ├── genome.ltrfinder.five_prime_LTR.fa ├── genome.ltrfinder.seq.fa ├── genome.ltrfinder.seq.fa.split │ ├── 001 │ │ ├── genome.ltrfinder.seq.part-001.fa │ │ ├── genome.ltrfinder.seq.part-001.fa.classified │ │ └── genome.ltrfinder.seq.part-001.fa.masked │ ├── 002 │ │ ├── genome.ltrfinder.seq.part-002.fa │ │ ├── genome.ltrfinder.seq.part-002.fa.classified │ │ └── genome.ltrfinder.seq.part-002.fa.masked │ └── 003 │ │ ├── genome.ltrfinder.seq.part-003.fa │ │ ├── genome.ltrfinder.seq.part-003.fa.classified │ │ └── genome.ltrfinder.seq.part-003.fa.masked ├── genome.ltrfinder.three_prime_LTR.fa ├── splitBYscaff │ ├── scaffold10278 │ │ └── scaffold10278.fa │ └── scaffold10747 │ │ └── scaffold10747.fa ├── test.genome.fa └── used_softwares │ ├── dawgpaws │ ├── apollo │ │ ├── wheat.style │ │ └── wheat.tiers │ ├── docs │ │ ├── TiersGuide.doc │ │ ├── gpl.txt │ │ └── html │ │ │ ├── css │ │ │ ├── dawgpaws.css │ │ │ └── dawgpaws_man.css │ │ │ ├── images │ │ │ ├── DAWGPAWS_med.png │ │ │ └── dawgpaws.ico │ │ │ ├── index.html │ │ │ ├── man.html │ │ │ ├── man │ │ │ ├── batch_blast.html │ │ │ ├── batch_eugene.html │ │ │ ├── batch_findgaps.html │ │ │ ├── batch_findltr.html │ │ │ ├── batch_findmite.html │ │ │ ├── batch_geneid.html │ │ │ ├── batch_genemark.html │ │ │ ├── batch_genscan.html │ │ │ ├── batch_hardmask.html │ │ │ ├── batch_hmmer.html │ │ │ ├── batch_ltrfinder.html │ │ │ ├── batch_ltrseq.html │ │ │ ├── batch_repmask.html │ │ │ ├── batch_tenest.html │ │ │ ├── batch_trf.html │ │ │ ├── clust_write_shell.html │ │ │ ├── cnv_blast2gff.html │ │ │ ├── cnv_fgenesh2gff.html │ │ │ ├── cnv_findltr2gff.html │ │ │ ├── cnv_game2gff3.html │ │ │ ├── cnv_genemark2gff.html │ │ │ ├── cnv_gff2game.html │ │ │ ├── cnv_ltrfinder2gff.html │ │ │ ├── cnv_ltrseq2gff.html │ │ │ ├── cnv_ltrstruc2gff.html │ │ │ ├── cnv_repmask2gff.html │ │ │ ├── cnv_repseek2gff.html │ │ │ ├── cnv_seq2dir.html │ │ │ ├── cnv_tenest2gff.html │ │ │ ├── dir_merge.html │ │ │ ├── fasta_merge.html │ │ │ ├── fasta_shorten.html │ │ │ ├── fetch_tenest.html │ │ │ ├── gff_seg.html │ │ │ ├── ltrstruc_prep.html │ │ │ ├── seq_oligocount.html │ │ │ └── vennseq.html │ │ │ └── svn-commit.tmp~ │ ├── emacs_modes │ │ ├── apollo-config-mode.el │ │ ├── apollo-styles-mode.el │ │ └── apollo-tiers-mode.el │ ├── scripts │ │ ├── batch_blast.pl │ │ ├── batch_eugene.pl │ │ ├── batch_findgaps.pl │ │ ├── batch_findltr.pl │ │ ├── batch_findmite.pl │ │ ├── batch_geneid.pl │ │ ├── batch_genemark.pl │ │ ├── batch_genscan.pl │ │ ├── batch_hardmask.pl │ │ ├── batch_hmmer.pl │ │ ├── batch_ltrfinder.pl │ │ ├── batch_ltrfinder.pl~ │ │ ├── batch_ltrseq.pl │ │ ├── batch_repmask.pl │ │ ├── batch_tenest.pl │ │ ├── batch_trf.pl │ │ ├── clust_write_shell.pl │ │ ├── cnv_blast2gff.pl │ │ ├── cnv_fgenesh2gff.pl │ │ ├── cnv_findltr2gff.pl │ │ ├── cnv_game2gff3.pl │ │ ├── cnv_genemark2gff.pl │ │ ├── cnv_gff2game.pl │ │ ├── cnv_ltrfinder2gff.pl │ │ ├── cnv_ltrseq2gff.pl │ │ ├── cnv_ltrstruc2gff.pl │ │ ├── cnv_repmask2gff.pl │ │ ├── cnv_repseek2gff.pl │ │ ├── cnv_seq2dir.pl │ │ ├── cnv_tenest2gff.pl │ │ ├── config │ │ │ ├── batch_blast_full.jcfg │ │ │ ├── batch_blast_tab.jcfg │ │ │ ├── batch_findltr.jcfg │ │ │ ├── batch_hmmer.jcfg │ │ │ ├── batch_ltrfinder.jcfg │ │ │ ├── batch_ltrfinder.jcfg~ │ │ │ ├── batch_mask.jcfg │ │ │ ├── batch_oligocount.jcfg │ │ │ ├── findmite_params.jcfg │ │ │ ├── findmite_params.txt │ │ │ └── hex_eugene.par │ │ ├── dir_merge.pl │ │ ├── extract_pod.pl │ │ ├── fasta_dirsplit.pl │ │ ├── fasta_merge.pl │ │ ├── fasta_shorten.pl │ │ ├── fetch_tenest.pl │ │ ├── gff_seg.pl │ │ ├── ltrstruc_prep.pl │ │ ├── seq_oligocount.pl │ │ └── vennseq.pl │ └── t │ │ ├── data │ │ ├── HEX3045G05 │ │ │ ├── HEX3045G05.game.xml.gz │ │ │ ├── HEX3045G05_TREP9.masked.fasta │ │ │ ├── HEX3045G05_ann_test.game.xml │ │ │ ├── blast │ │ │ │ ├── HEX3045G05_AcTA_1.bln │ │ │ │ ├── HEX3045G05_AsPUT_157.bln │ │ │ │ ├── HEX3045G05_AsTA_1.bln │ │ │ │ ├── HEX3045G05_AsTA_1.blx │ │ │ │ ├── HEX3045G05_AtGI_13.bln │ │ │ │ ├── HEX3045G05_AtUniGene_56.bln │ │ │ │ ├── HEX3045G05_AvenSatTA_2.bln │ │ │ │ ├── HEX3045G05_FaTA_2.bln │ │ │ │ ├── HEX3045G05_HvUniGene_47.bln │ │ │ │ ├── HEX3045G05_OsUniGene_65.bln │ │ │ │ ├── HEX3045G05_SbGI_8.bln │ │ │ │ ├── HEX3045G05_SbPUT_157.bln │ │ │ │ ├── HEX3045G05_SbTA_2.bln │ │ │ │ ├── HEX3045G05_SbUniGene_21.bln │ │ │ │ ├── HEX3045G05_ShTA_2.bln │ │ │ │ ├── HEX3045G05_ShTA_2.blx │ │ │ │ ├── HEX3045G05_SoUniGene_8.bln │ │ │ │ ├── HEX3045G05_SpPUT_157.bln │ │ │ │ ├── HEX3045G05_SpPUT_157.blx │ │ │ │ ├── HEX3045G05_SpTA_2.bln │ │ │ │ ├── HEX3045G05_SpTA_2.blx │ │ │ │ ├── HEX3045G05_TmPUT_157.bln │ │ │ │ ├── HEX3045G05_TmTA_2.bln │ │ │ │ ├── HEX3045G05_TtTA_1.bln │ │ │ │ └── HEX3045G05_ZmUniGene_61.bln │ │ │ ├── fgenesh │ │ │ │ ├── fgenesh.txt │ │ │ │ ├── fgenesh_html.txt │ │ │ │ ├── fgenesh_result.gff │ │ │ │ └── fgenesh_txt_save.txt │ │ │ ├── find_ltr │ │ │ │ ├── HEX3045G05_findltr_def.ltrseq │ │ │ │ ├── HEX3045G05_findltr_def.txt │ │ │ │ ├── HEX3045G05_findltr_old.ltrseq │ │ │ │ ├── HEX3045G05_findltr_old.txt │ │ │ │ ├── HEX3045G05_findltr_older.ltrseq │ │ │ │ └── HEX3045G05_findltr_older.txt │ │ │ ├── findmite │ │ │ │ ├── HEX3045G05.ta.findmite │ │ │ │ ├── HEX3045G05_TA_11.mite.txt │ │ │ │ ├── HEX3045G05_TA_11mite.gff │ │ │ │ ├── HEX3045G05_TA_12.mite.txt │ │ │ │ ├── HEX3045G05_TA_12mite.gff │ │ │ │ ├── HEX3045G05_TA_13.mite.txt │ │ │ │ └── HEX3045G05_TA_13mite.gff │ │ │ ├── gene │ │ │ │ ├── HEX3045G05.genscan.gff │ │ │ │ └── HEX3045G05.genscan.out │ │ │ ├── genemark │ │ │ │ ├── HEX3045G05_genemark_hv.out │ │ │ │ ├── HEX3045G05_genemark_os.out │ │ │ │ ├── HEX3045G05_genemark_ta.out │ │ │ │ └── HEX3045G05_genemark_zm.out │ │ │ ├── gff │ │ │ │ ├── HEX3045G05.genscan.gff │ │ │ │ ├── HEX3045G05_TREP9_EL.gff │ │ │ │ ├── HEX3045G05_all_blast.gff.gz │ │ │ │ ├── HEX3045G05_gaps.gff │ │ │ │ ├── HEX3045G05_genemark_hv.gff │ │ │ │ ├── HEX3045G05_genemark_os.gff │ │ │ │ ├── HEX3045G05_genemark_ta.gff │ │ │ │ ├── HEX3045G05_genemark_zm.gff │ │ │ │ └── HEX3045G05_tenest.gff │ │ │ ├── ltr_finder │ │ │ │ ├── HEX3045G05_def_ltr_finder.txt │ │ │ │ ├── HEX3045G05_p_10_ltr_finder.txt │ │ │ │ └── HEX3045G05_p_30_ltr_finder.txt │ │ │ ├── ltr_seq │ │ │ │ └── HEX3045G05_ltrseq.txt │ │ │ ├── ltr_struc │ │ │ │ ├── .svn │ │ │ │ │ ├── all-wcprops │ │ │ │ │ ├── entries │ │ │ │ │ ├── format │ │ │ │ │ └── text-base │ │ │ │ │ │ ├── HEX3045G0513370_RT3_B31_L46_184_fsta.txt.svn-base │ │ │ │ │ │ ├── HEX3045G0513370_RT3_B31_L46_184_orfs.txt.svn-base │ │ │ │ │ │ ├── HEX3045G0513370_RT3_B31_L46_184_rprt.txt.svn-base │ │ │ │ │ │ ├── HEX3045G0513370_RT3_B31_L46_184_trns.txt.svn-base │ │ │ │ │ │ ├── HEX3045G0517999_RT7_B17_L22_183_fsta.txt.svn-base │ │ │ │ │ │ ├── HEX3045G0517999_RT7_B17_L22_183_orfs.txt.svn-base │ │ │ │ │ │ ├── HEX3045G0517999_RT7_B17_L22_183_rprt.txt.svn-base │ │ │ │ │ │ ├── HEX3045G0517999_RT7_B17_L22_183_trns.txt.svn-base │ │ │ │ │ │ ├── HEX3045G05_6933_RT3_B2_L6_185_fsta.txt.svn-base │ │ │ │ │ │ ├── HEX3045G05_6933_RT3_B2_L6_185_orfs.txt.svn-base │ │ │ │ │ │ ├── HEX3045G05_6933_RT3_B2_L6_185_rprt.txt.svn-base │ │ │ │ │ │ └── HEX3045G05_6933_RT3_B2_L6_185_trns.txt.svn-base │ │ │ │ ├── HEX3045G0513370_RT3_B31_L46_184_fsta.txt │ │ │ │ ├── HEX3045G0513370_RT3_B31_L46_184_orfs.txt │ │ │ │ ├── HEX3045G0513370_RT3_B31_L46_184_rprt.txt │ │ │ │ ├── HEX3045G0513370_RT3_B31_L46_184_trns.txt │ │ │ │ ├── HEX3045G0517999_RT7_B17_L22_183_fsta.txt │ │ │ │ ├── HEX3045G0517999_RT7_B17_L22_183_orfs.txt │ │ │ │ ├── HEX3045G0517999_RT7_B17_L22_183_rprt.txt │ │ │ │ ├── HEX3045G0517999_RT7_B17_L22_183_trns.txt │ │ │ │ ├── HEX3045G05_6933_RT3_B2_L6_185_fsta.txt │ │ │ │ ├── HEX3045G05_6933_RT3_B2_L6_185_orfs.txt │ │ │ │ ├── HEX3045G05_6933_RT3_B2_L6_185_rprt.txt │ │ │ │ └── HEX3045G05_6933_RT3_B2_L6_185_trns.txt │ │ │ ├── repseek │ │ │ │ ├── repseek_l20.txt │ │ │ │ └── repseek_l25.txt │ │ │ ├── rm │ │ │ │ ├── HEX3045G05_ALLDB.rm.gff │ │ │ │ ├── HEX3045G05_TREP9.masked.fasta │ │ │ │ ├── HEX3045G05_TREP9.rm.cat │ │ │ │ ├── HEX3045G05_TREP9.rm.out │ │ │ │ └── HEX3045G05_TREP9_EL.gff │ │ │ └── tenest │ │ │ │ ├── 1188415018_5205.LTR │ │ │ │ ├── 1188415018_5205.svg │ │ │ │ ├── HEX3045G05.LTR │ │ │ │ └── HEX3045G05.svg.xml │ │ ├── WHEAT_TEST │ │ │ ├── CON-1 │ │ │ │ ├── Ames │ │ │ │ ├── Angela │ │ │ │ ├── Bagy │ │ │ │ ├── Barbara │ │ │ │ ├── Claudia │ │ │ │ └── Daniela │ │ │ ├── LTRs │ │ │ │ ├── Ames-0.fasta │ │ │ │ ├── Angela-0.fasta │ │ │ │ ├── Bagy-0.fasta │ │ │ │ ├── Barbara-0.fasta │ │ │ │ ├── Claudia-0.fasta │ │ │ │ └── Daniela-0.fasta │ │ │ ├── TEs │ │ │ │ ├── Ames │ │ │ │ ├── Angela │ │ │ │ ├── Bagy │ │ │ │ ├── Barbara │ │ │ │ ├── Claudia │ │ │ │ └── Daniela │ │ │ ├── ltr_list │ │ │ ├── unique_repeats │ │ │ ├── unique_repeats.csq │ │ │ ├── unique_repeats.nhd │ │ │ └── unique_repeats.ntb │ │ ├── blast │ │ │ ├── SanMiguel_200610.nhr │ │ │ ├── SanMiguel_200610.nin │ │ │ ├── SanMiguel_200610.nsq │ │ │ ├── TREP9_nr.nhr │ │ │ ├── TREP9_nr.nin │ │ │ └── TREP9_nr.nsq │ │ ├── config │ │ │ ├── LTR.cfg │ │ │ ├── LTR_400_8000.cfg │ │ │ ├── batch_blast_tab.jcfg │ │ │ ├── batch_findltr.jcfg │ │ │ ├── batch_hmmer.jcfg │ │ │ ├── batch_ltrfinder.jcfg │ │ │ ├── batch_ltrseq.jcfg │ │ │ ├── batch_mask.jcfg │ │ │ ├── findmite_params.jcfg │ │ │ ├── geneid_wheat.param │ │ │ └── hex_eugene.par │ │ ├── exp │ │ │ ├── HEX2903P03.geneid.gff │ │ │ ├── HEX2903P03.genscan.gff │ │ │ ├── HEX2903P03.tenest.gff │ │ │ ├── HEX2903P03_SanMiguel_200610.bln │ │ │ ├── HEX2903P03_TREP9_nr.bln │ │ │ ├── HEX2903P03_blast.gff │ │ │ ├── HEX2903P03_def_ltr_finder.gff │ │ │ ├── HEX2903P03_eugene.gff │ │ │ ├── HEX2903P03_findltr_Def.gff │ │ │ ├── HEX2903P03_gaps.gff │ │ │ ├── HEX2903P03_hmm_dp_test.gff │ │ │ ├── HEX2903P03_rm_TREP9.gff │ │ │ ├── HEX2903P03_trf.gff │ │ │ ├── HEX2986I03.geneid.gff │ │ │ ├── HEX2986I03.genscan.gff │ │ │ ├── HEX2986I03.tenest.gff │ │ │ ├── HEX2986I03_SanMiguel_200610.bln │ │ │ ├── HEX2986I03_TREP9_nr.bln │ │ │ ├── HEX2986I03_blast.gff │ │ │ ├── HEX2986I03_def_ltr_finder.gff │ │ │ ├── HEX2986I03_eugene.gff │ │ │ ├── HEX2986I03_findltr_Def.gff │ │ │ ├── HEX2986I03_gaps.gff │ │ │ ├── HEX2986I03_hmm_dp_test.gff │ │ │ ├── HEX2986I03_rm_TREP9.gff │ │ │ ├── HEX2986I03_trf.gff │ │ │ ├── HEX3045G05.geneid.gff │ │ │ ├── HEX3045G05.genscan.gff │ │ │ ├── HEX3045G05.tenest.gff │ │ │ ├── HEX3045G05_SanMiguel_200610.bln │ │ │ ├── HEX3045G05_TA_11mite.gff │ │ │ ├── HEX3045G05_TA_12mite.gff │ │ │ ├── HEX3045G05_TA_13mite.gff │ │ │ ├── HEX3045G05_TREP9_nr.bln │ │ │ ├── HEX3045G05_blast.gff │ │ │ ├── HEX3045G05_def_ltr_finder.gff │ │ │ ├── HEX3045G05_eugene.gff │ │ │ ├── HEX3045G05_findltr_Def.gff │ │ │ ├── HEX3045G05_gaps.gff │ │ │ ├── HEX3045G05_gff3.gff │ │ │ ├── HEX3045G05_gff3_withseq.gff │ │ │ ├── HEX3045G05_hmm_dp_test.gff │ │ │ ├── HEX3045G05_ltrseq_default.gff │ │ │ ├── HEX3045G05_ltrseq_dist_400_8000.gff │ │ │ ├── HEX3045G05_rm_TREP9.gff │ │ │ ├── HEX3045G05_trf.gff │ │ │ ├── blast_cnv_expected.txt │ │ │ ├── fgenesh_cnv_expected.txt │ │ │ ├── findltr_cnv_expected.txt │ │ │ ├── genemark_cnv_expected.txt │ │ │ ├── genscan_gamexml_expected.txt │ │ │ ├── gff_seg_50x_expected.txt │ │ │ ├── ltrfinder_cnv_expected.txt │ │ │ ├── ltrseq_cnv_expected.txt │ │ │ ├── repeatmasker_cnv_expected.txt │ │ │ ├── repseek_cnv_expected.txt │ │ │ ├── tenest_cnv_expected.txt │ │ │ └── venn_test_result.txt │ │ ├── fasta │ │ │ ├── HEX2903P03.masked.fasta │ │ │ ├── HEX2986I03.masked.fasta │ │ │ └── HEX3045G05.masked.fasta │ │ ├── fasta_sample │ │ │ ├── HEX2903P03_sample.fasta │ │ │ ├── HEX2986I03_sample.fasta │ │ │ └── HEX3045G05_sample.fasta │ │ ├── hmm_models │ │ │ ├── Stowaway14.hmm │ │ │ ├── Stowaway14_rc.hmm │ │ │ ├── Tourist4.hmm │ │ │ ├── Tourist4_rc.hmm │ │ │ ├── adh_L.hmm │ │ │ └── adh_L_rc.hmm │ │ ├── oligo_count │ │ │ └── gff_seg_test_in.gff │ │ ├── repmask │ │ │ └── TREP9.nr.fasta │ │ └── venn_test │ │ │ ├── 1trf.ap.gff │ │ │ ├── 2eugOs.ap.gff │ │ │ ├── 2fGh.ap.gff │ │ │ ├── 2gID.ap.gff │ │ │ ├── 2gmHv.ap.gff │ │ │ ├── 2gmOs.ap.gff │ │ │ ├── 2gmTa.ap.gff │ │ │ ├── 2gmZm.ap.gff │ │ │ ├── HEX3045G05_TREP9.masked.fasta │ │ │ └── test_venn.txt │ │ ├── dp_batch_blast_test.t │ │ ├── dp_batch_eugene_test.t │ │ ├── dp_batch_findltr_test.t │ │ ├── dp_batch_findmite_test.t │ │ ├── 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