├── .gitignore ├── 00.scripts ├── QualityControlAndMergeReads.pl ├── bam_sta.pl ├── calculate_dxy.pl ├── clean_shared_memory.pl ├── convertNEXUS2newick.pl ├── distanceMatrixCalculator.pl ├── extract_roh.pl ├── fastaFileStatics_NoBioPerl.pl ├── fastq2fasta.pl ├── fastq_quality_check.pl ├── fix_consensus.pl ├── get_0fold-4fold_sites.pl ├── get_len.pl ├── gff2cds.pl ├── gff2cds.pl.GFF_STA.pl ├── gff2cds.py ├── gff_length_sta.pl ├── ibd_sta.pl ├── nanopore_fasta_statistics.pl ├── nanopore_filter_fastq.pl ├── overlap_lst.pl ├── pick_longest_ensembl.pl ├── pick_longest_ncbi.pl ├── random_extract_fasta.pl ├── read_fasta.pl ├── readingFasta.pl ├── readingFasta_NoBioPerl.pl ├── readingFasta_sub.pl ├── remove_low_support_nodes.pl ├── server_stat.pl ├── split_fasta.pl ├── split_task.pl ├── split_vcf.pl ├── thin_vcf.pl ├── transcriptome_reads_count.pl ├── translateCDS2Protein.pl ├── vcf_beagle2chromopainter.pl ├── vcf_extractBed.pl └── vcf_remove_ind.pl ├── 01.dadi_fsc ├── 00.convertWithFSC │ ├── convertAngsd2Fsc.pl │ ├── convertDadi2Fsc.pl │ ├── convertFsc2Dadi.pl │ ├── convertVcf2Fsc.pl │ └── convert_vcf_to_dadi_input.pl ├── 01.data2fs │ ├── 01.split_reading.pl │ ├── 02.convert.pl │ ├── 03.gather.pl │ ├── convert.pl │ └── convert.py ├── 02.two_pop_model │ ├── 01.IpreExp │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ └── custom_model.py │ ├── 02.MpreExp │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ └── 03.collect.pl │ ├── 03.M_IpreExp │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ └── custom_model.py │ ├── 04.Ipre │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ └── custom_model.py │ ├── 05.Mpre │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ └── custom_model.py │ ├── 06.M_Ipre │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ └── custom_model.py │ ├── 07.IMpre_RecentBottleneck │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ └── custom_model.py │ ├── 08.IMexp_RecentBottleneck │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ ├── custom_model.py │ │ ├── dadi.fs │ │ └── effective.len │ ├── 09.changePop1First │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ ├── custom_model.py │ │ ├── custom_model.pyc │ │ ├── dadi.fs │ │ ├── effective.len │ │ └── model_10.pdf │ └── 10.changePop2First │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ ├── custom_model.py │ │ ├── custom_model.pyc │ │ ├── dadi.fs │ │ ├── effective.len │ │ └── model_10.pdf ├── 03.bootstrap │ ├── 01.generate_fs.py │ ├── 02.run.pl │ └── 03.collect.pl ├── 04.one_pop_model │ ├── 01.4Stage │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ └── custom_model.py │ └── 02.2Stage │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ ├── custom_model.py │ │ ├── dadi.fs │ │ └── effective.len ├── 05.fsc_onepop │ ├── clear.pl │ ├── model.est │ ├── model.tpl │ ├── model_DAFpop0.obs │ └── run.pl ├── 06.dadi_gene_flow_comparision │ ├── model_Consistent_instantPop1ToPop2_geneflow │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ ├── custom_model.py │ │ ├── dadi.fs │ │ └── effective.len │ ├── model_Consistent_instantPop2ToPop1_geneflow │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ ├── custom_model.py │ │ ├── dadi.fs │ │ └── effective.len │ ├── model_consistent_exp │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ ├── custom_model.py │ │ ├── dadi.fs │ │ └── effective.len │ ├── model_consistent_geneflow │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ ├── custom_model.py │ │ ├── dadi.fs │ │ └── effective.len │ ├── model_instantPop1ToPop2_geneflow │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ ├── custom_model.py │ │ ├── dadi.fs │ │ └── effective.len │ ├── model_instantPop2ToPop1_geneflow │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ ├── custom_model.py │ │ ├── dadi.fs │ │ └── effective.len │ └── model_no_geneflow │ │ ├── 01.model.py │ │ ├── 02.run.pl │ │ ├── 03.collect.pl │ │ ├── custom_model.py │ │ ├── dadi.fs │ │ └── effective.len ├── 07.fsc_two_pop │ ├── 01.no_gene_flow │ │ ├── clear.pl │ │ ├── model.est │ │ ├── model.tpl │ │ ├── model_jointMAFpop1_0.obs │ │ └── run.pl │ └── 02.gene_flow │ │ ├── clear.pl │ │ ├── model.est │ │ ├── model.tpl │ │ ├── model_jointMAFpop1_0.obs │ │ └── run.pl └── fastsimcoal2 │ ├── 01.sta.pl │ ├── convertDadi2Fsc.pl │ ├── convertVcf2Fsc.pl │ ├── simple_configure_checker.pl │ ├── topology_01 │ └── T1_G3 │ │ ├── clear.pl │ │ ├── model.est │ │ ├── model.par │ │ ├── model.tpl │ │ ├── model_jointMAFpop1_0.obs │ │ ├── model_jointMAFpop2_0.obs │ │ ├── model_jointMAFpop2_1.obs │ │ ├── model_jointMAFpop3_0.obs │ │ ├── model_jointMAFpop3_1.obs │ │ ├── model_jointMAFpop3_2.obs │ │ └── run.pl │ └── vcf2maf.pl ├── 02.manual_check_gene ├── 00.mkdb.sh ├── 01.blast.sh ├── 02.genewise.sh ├── 03.convert_genewise2gff.pl └── utils │ └── get_seq_from_genome.pl ├── 03.treemix ├── 01.convert.pl └── 02.treemix.pl ├── 04.saguarogw ├── 01.convert.sh ├── 02.sta.pl ├── 03.convert_tree.sh ├── 04.build_tree.pl └── 05.plot_along_chromosome.pl ├── 05.beagleAndHWE ├── 01.beagle │ ├── 01.selectInd.pl │ └── 02.phase.sh └── 02.HWE │ ├── 01.filterHWE.sh │ ├── 02.ref_alt_correction.pl │ └── 03.combine.pl ├── 06.smcpp ├── 01.index.sh ├── 02.convert.pl ├── 03.estimate.pl ├── 04.plot.pl ├── 05.split.pl └── 06.split_plot.pl ├── 07.chloroplast_assembly ├── 01.gb2tbl.pl └── linux64.tbl2asn.gz ├── 08.stairway_plot ├── 01.prepare.sh ├── 02.ready2go.pl ├── 03.Step2.pl ├── pro.blueprint └── stairway_plot_es │ ├── GRAL_VectorGraphics2D_license.txt │ ├── SFS_log_likelihood_problem_no_dim_penalty5.class │ ├── SFS_log_likelihood_problem_no_dim_penalty6.class │ ├── Stairbuilder.class │ ├── Stairpainter.class │ ├── Stairway_fold_training_testing5.class │ ├── Stairway_output_summary_plot.class │ ├── Stairway_unfold_training_testing5.class │ ├── SwarmOps_license.txt │ ├── VectorGraphics2D-0.9.3.jar │ ├── example │ ├── README.pdf │ ├── two-epoch.blueprint │ └── two-epoch_fold.blueprint │ ├── gral-core-0.11.jar │ └── swarmops.jar ├── 09.psmc ├── 01.cns.sh ├── 02.psmc_step1.sh ├── 03.psmc_step2.sh ├── 04.psmc_step3.pl └── 05.plot.sh ├── 10.ihs ├── 00.phase.sh ├── 01.convert.pl ├── 02.selscan.pl ├── 02.selscan.pl.sh ├── 03.norm.sh ├── 04.ihs.pl └── vcf_remove_ind.pl ├── 11.samtools_callSNP ├── 01.call_snp.pl ├── 02.filter_indel.pl ├── 03.filter_dp_qual.pl ├── 04.merge.pl ├── 05.filter_repeat.pl ├── 06.get_autosome.pl ├── filter_dp_qual.pl └── filter_indel.pl ├── 12.mutation_number ├── 00.cat.sh ├── 01.clean.pl ├── 02.prepareAndRun.sh ├── 03.generate_seq.pl ├── 04.count.pl ├── baseml.ctl ├── mega │ ├── count_mutation_number_relative_to_ancestor.pl │ └── readme.txt └── scripts │ └── Gblocks2Paml.pl ├── 15.GO_analysis ├── 00.resources │ ├── 01.LeafToRoot.pl │ └── Permanent.URL ├── 01.go_annotation │ ├── 02.uplevel.pl │ ├── 02.uplevel.pl~ │ ├── extract_go_from_gb_file.pl │ └── trim.pl └── 02.go_enrichment │ ├── 00.generate_list.pl │ ├── 01.GoEnrichment.pl │ └── 02.GoSignificant.pl ├── 16.maf2positive_selection ├── 01.link.pl ├── 02.prepare.paml.create.tree.pl ├── 03.prepare.paml.create.CTL.pl ├── 04.paml.pl ├── ctl │ ├── branch-site.an.fix.ctl │ ├── branch-site.an.nofix.ctl │ ├── branch-site.ds.fix.ctl │ ├── branch-site.ds.nofix.ctl │ ├── branch-site.ss.fix.ctl │ ├── branch-site.ss.nofix.ctl │ ├── branch.freeratio.ctl │ ├── branch.oneratio.ctl │ ├── branch.tworatio.an.ctl │ ├── branch.tworatio.ds.ctl │ ├── branch.tworatio.ss.ctl │ └── ctl.template ├── input.tre ├── scripts │ ├── Gblocks2Paml.pl │ └── filter_stop_codon.pl ├── statistics │ ├── 01.freeratio │ │ ├── 01.get.freeratio.result.pl │ │ └── 02.rand.plot.pl │ ├── 02.branch │ │ ├── 01.get.branch.result.pl │ │ ├── 02.chi2.pl │ │ ├── 03.fdr.pl │ │ └── sta.pl │ └── 03.branch-site │ │ ├── 01.get.brachsite.result.pl │ │ ├── 02.chi2.pl │ │ ├── 03.fdr.pl │ │ └── sta.pl └── tree │ ├── tree.an │ ├── tree.ds │ ├── tree.raw │ └── tree.ss ├── 17.gwas ├── 01.plink │ ├── 01.convert.sh │ ├── 02.rename_bim.pl │ ├── 03.extract.sh │ ├── 04.transform.pl │ ├── 05.associate.sh │ ├── 06.plot.pl │ ├── 07.plot.R │ └── phenotype.txt ├── 02.emmax │ ├── 00.rename_bim.pl │ ├── 01.convert.sh │ ├── 02.king.sh │ ├── 03.cor.sh │ ├── 04.plot.pl │ ├── 05.plot.R │ └── plink.phen └── 03.gemma │ ├── 00.convert.sh │ ├── 01.transform.pl │ ├── 02.basic.sh │ ├── 03.plot.pl │ ├── 04.plot.R │ └── phenotype.txt ├── 18.maf_related_scripts ├── 01.distance │ ├── 01.convertMaf2List.pl │ ├── 02.calculate_distance.pl │ ├── 03.plot.pl │ └── scripts │ │ └── plot.pl ├── 02.maf_based_assembly │ ├── 01.transfer.pl │ └── alignment.maf ├── convert_coordinate.pl ├── convert_mafList2VCF.pl ├── length_summary.pl ├── multiz.sh ├── point2gff.pl ├── rename.pl ├── roast.sh └── syntenyPlotter │ ├── 00.prepare.pl │ └── 01.syntenyPlotter.pl ├── 19.kegg_analysis ├── 01.standardization.pl ├── 02.KEGGenrichment.pl ├── 03.filter.pl ├── filter.pl ├── kegg.map └── query.ko ├── 20.pseudogene ├── 00.maf_project.sh ├── 01.convertMaf2ListFull.pl └── 02.lst2gene.pl ├── 22.ibd_analysis ├── 00.split_vcf.pl ├── 01.ibd.pl ├── 02.merge.sh ├── 03.ibd_sta.pl ├── 04.rename.pl ├── order.txt └── pop.lst ├── 24.transcriptome ├── 01.cut_cds │ ├── 01.extract_cds.pl │ ├── 02.mafft.pl │ ├── 03.gblock.pl │ ├── 04.convertGb2bed.pl │ ├── 05.collectBED.pl │ └── scripts │ │ ├── convertHTM.pl │ │ └── extractBed.pl └── 02.count │ ├── 01.combine.pl │ ├── 02.rename.pl │ ├── speciesA │ ├── 01.count.pl │ ├── 02.collect.pl │ └── scripts │ │ └── sam2reads_count.pl │ └── tissue.lst ├── 25.inparanoid-ghostz ├── BLOSUM45 ├── BLOSUM62 ├── BLOSUM80 ├── EC ├── LICENCE ├── PAM30 ├── PAM70 ├── README ├── SC ├── blast_parser.pl ├── ghostz_parser.pl ├── inparanoid.pl ├── one2one.pl └── seqstat.jar ├── 26.kegg_enrichment ├── 01.generate_list.pl ├── 02.path.pl ├── 03.sta.pl ├── 04.sta_withThreeTest.pl └── gene.path ├── 27.fastEPRR ├── 00.phase.sh ├── 01.split_vcf.pl ├── 02.fastEPRR.pl └── 03.transformat.pl ├── 28.phylogeny_reconstruction ├── 00.reroot │ ├── filterTreeThatIsNotRootedCorrectly.pl │ └── reroot.cmd ├── 01.mpest │ ├── 01.generate_control_file.pl │ ├── 02.generate_bootstrap_input.pl │ ├── 03.run_bootstrap.pl │ ├── 04.convertAndCollect.pl │ ├── convertNEXUS2newick.pl │ ├── count_tre.pl │ ├── merge_count.pl │ └── unifyTreeLength.pl ├── 02.ASTRAL │ ├── 00.consensus.seq.len.pl │ ├── 00.generate.ANC.fasta.pl │ ├── 01.get.seq.from.bed.pl │ ├── 01.get.seq.from.bed.pl.sh │ ├── 02.cds.info.pl │ ├── 03.select.pl │ ├── 03.select.pl.extract.pl │ ├── Ore.final.gff3.CDS.bed │ └── keep_id_list.txt ├── 03.densitree_vcf │ ├── 01.convert.vcf2faByWind.pl │ ├── 02.raxml.pl │ ├── 03.fasttree.pl │ ├── 04.reroot.pl │ ├── 05.nclock2clock.pl │ └── unify_length.py ├── 04.maf_gene_tree │ ├── 01.convertMaf2List.pl │ ├── 02.lst2gene.pl │ ├── 03.raxml.pl │ ├── 04.collect_high_confidence.pl │ ├── 05.nclock2clock.pl │ ├── 06.count.pl │ ├── 07.calculate_distance.pl │ ├── clear_gff.pl │ ├── gene_sta.pl │ └── sta.pl ├── 05.examl_bootstrap │ ├── 01.examl_pipeline.pl │ └── get_best_tree.pl ├── 06.phylogeny_heterogeneity │ ├── 01.filter.pl │ ├── 02.droptip.R │ ├── 03.count.pl │ ├── 04.classify.pl │ ├── 05.plot.pl │ └── origin.tre └── 07.tree_classify │ ├── 01.count.pl │ └── 02.classfy.pl ├── 29.pantherAnalysis ├── 01.runpanther │ ├── 01.splitfasta.sh │ └── 02.runPanther.pl └── 02.convertFormat │ ├── 01.extract_DirectRun.pl │ ├── 01.extract_Download.sh │ └── 01.extract_InterProScan.pl ├── 30.divergence_time_mcmctree ├── 00.readme.txt ├── 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 ├── 31.gene_charactor_calculate ├── 00.gff.trans2gene.list ├── 01.len.pl ├── 02.Gene.stat.pl ├── 02.Gene.stat.pl.CDS.len.txt ├── 02.Gene.stat.pl.Exon.len.txt ├── 02.Gene.stat.pl.Exon.num.txt ├── 02.Gene.stat.pl.Intron.len.txt ├── 02.Gene.stat.pl.mRNA.len.txt ├── 03.plot.pl ├── 03.plot.pl.R ├── 03.plot.pl.pdf ├── 04.average.pl ├── 04.average.pl.out ├── cow_test.gff ├── cow_test.trans2gene.len.txt ├── py_test.gff ├── py_test.trans2gene.len.txt ├── sheep_test.gff └── sheep_test.trans2gene.len.txt ├── 32.mafExtractGene_keepGenesFromGff ├── 01.convert_coordinate.pl ├── 02.get_valid_gene_id.pl ├── 03.get_protein_id.pl └── gff │ ├── ds.gff │ ├── gac.gff │ └── tor.gff ├── 33.merge_gff ├── ConvertFormat_augustus.pl └── Merge.gff.pl ├── 34.hyphy ├── 01.gblock.pl ├── 02.flt.stop_codon.pl ├── 03.hyphy.aBSREL.pl ├── 04.extract_aBSREL.pl ├── 05.hyphy.BUSTED.pl ├── example_raw_input │ └── cds.fa └── scripts │ └── extract_aBSREL.pl ├── 35.novel_gene ├── 01.basedOnMaf │ ├── 01.getPoint2Point.pl │ ├── 02.novel_gene.pl │ └── 03.filter.pl └── 02.basetOnGhostz │ └── 01.new_gene.pl ├── 36.reseq_pipeline ├── 00.mappability │ ├── 01.index.sh │ ├── 02.mappability.sh │ ├── 03.wig_file.sh │ ├── 04.convert.sh │ ├── 05.keepBed.sh │ └── scripts │ │ └── BigWig2Bed.pl ├── 02.bwa_mem │ ├── 01.alignment.pl │ ├── 02.collect.pl │ ├── 03.rmDup.pl │ ├── 04.index.pl │ ├── 05.realn.pl │ ├── 06.align_sta.pl │ ├── 07.depth_info.pl │ ├── align_statistics.pl │ └── check_depth.pl ├── 03.call_snp │ ├── 01.gatk_haplotyper │ │ ├── 01.generateIntervals.pl │ │ ├── 02.integrate.pl │ │ ├── 03.merge_window.pl │ │ ├── 04.extractBiAllelicVar.pl │ │ └── 05.filter4essentialAnalysis.pl │ ├── distance_vcf.pl │ ├── hete_count.pl │ └── hete_count_window.pl ├── 03a.call_snp_haplotypeCaller │ ├── 01.HC.pl │ ├── 02.combinegvcf.pl │ ├── 03.hardfilter.pl │ ├── 04.merge_window.pl │ └── 05.filter.pl ├── 04.basicAnalysis │ ├── 01.njTree │ │ ├── 01.addOutGroup.pl │ │ ├── 02.vcf2bed.sh │ │ ├── 03.distance_matrix.sh │ │ └── 04.mdist2phylip.pl │ ├── 02.PCAanalysis │ │ ├── 01.pca.sh │ │ └── plot.pl │ ├── 03.kingship │ │ ├── 01.kingship.sh │ │ ├── 02.ggplot.pl │ │ ├── 03.filter_ind.pl │ │ └── 04.auto_remove_ind.pl │ ├── 04.admixture │ │ ├── 01.admixture.pl │ │ └── 04.ggplot2.pl │ ├── 05.ibd │ │ ├── 01.ibd.sh │ │ └── 02.ibd_sta.pl │ ├── 06.dxy │ │ ├── 01.calculate_dxy.pl │ │ └── keep.txt │ ├── 07.inbreeding │ │ └── 04.inbreeding.sh │ ├── 08.classify_vcf │ │ └── 02.classify.pl │ ├── 09.heta_statistic │ │ └── 06.hete.pl │ ├── 10.roh │ │ └── 07.roh.sh │ ├── change_bim_name.pl │ ├── vcf2bed.sh │ └── vcf_remove_ind.pl ├── 05.angsd │ ├── 01.step1.onePop │ │ ├── 00.ancestral.sh │ │ ├── 01.dosaf.sh │ │ ├── 02.sfs.sh │ │ ├── 03.theta.sh │ │ ├── 04.filterSite.pl │ │ ├── 05.calculate_theta_window.sh │ │ └── fixAncestral.pl │ ├── 02.step2.twoPop │ │ ├── 01.getSharedSites.sh │ │ ├── 02.realSFS.sh │ │ ├── 03.fst.sh │ │ └── 04.fst_window.sh │ └── 03.step3.threePop │ │ ├── 00.generatefilelist.pl │ │ ├── 01.getSharedSites.sh │ │ ├── 02.realSFS.threepop.sh │ │ ├── calculate_effectiveLen.pl │ │ └── keep.txt ├── 06.population_history │ ├── 01.psmc │ │ ├── 01.cns.sh │ │ ├── 02.psmc_step1.sh │ │ ├── 03.psmc_step2.sh │ │ ├── 04.psmc_step3.pl │ │ ├── 04.psmc_step3.pl.sh │ │ └── 05.plot.sh │ ├── 02.stairwayPlot │ │ ├── 01.prepare.sh │ │ ├── 02.ready2go.pl │ │ ├── 02.ready2go.pl.sh │ │ ├── 03.Step2.pl │ │ ├── 03.Step2.pl.sh │ │ ├── pda.blueprint │ │ ├── pda.blueprint.plot.sh │ │ ├── pda.blueprint.sh │ │ ├── pro.blueprint │ │ ├── pro.blueprint.plot.sh │ │ └── pro.blueprint.sh │ └── 03.smcpp │ │ ├── 01.index.sh │ │ ├── 02.convert.pl │ │ ├── 02.convert.pl.sh │ │ ├── 03.estimate.pl │ │ ├── 03.estimate.pl.sh │ │ ├── 04.plot.pl │ │ ├── 04.plot.pl.pdf │ │ ├── 04.plot.pl.sh │ │ ├── 05.split.pl │ │ ├── 05.split.pl.sh │ │ ├── 06.split_plot.pl │ │ ├── 06.split_plot.pl.sh │ │ └── pop.lst ├── 07.linkage_disequilibrium │ ├── 01.vcf2bed.sh │ ├── 02.calculate_r2.pl │ ├── 02.calculate_r2.pl.sh │ ├── 03.sta.pl │ ├── 04.merge.pl │ ├── 05.mean_ld.pl │ ├── calculate_decay.pl │ ├── calculate_mean.pl │ └── rename.pl ├── 09.recombination │ ├── 00.phase.sh │ ├── 01.split_vcf.pl │ ├── 02.fastEPRR.pl │ ├── 04.transFormat.pl │ └── remove_line1.pl ├── 10.genome_island │ ├── 01.merge.pl │ ├── 01.merge.pl.txt │ ├── 02.depmixS4.pl │ ├── 02.depmixS4.pl.Rscript │ ├── 02.depmixS4.pl.Rscript.log │ ├── 03.integrate_result.pl │ ├── 03.integrate_result.pl.txt │ ├── divergenceIsland.info │ ├── divergenceIsland.txt │ └── fst.txt └── 11.window_scan │ └── 01.window_scan.pl ├── 37.ensembl_dat_extract ├── extract_geneSymbolAndSeq.pl └── extract_go_from_gb_file.pl ├── 38.reference_based_assembly └── 01.generate_reference │ ├── 01.convertMaf2List.pl │ ├── 02.split_lst.pl │ ├── 03.convert2fa.pl │ ├── 04.collect.sh │ ├── 05.arrange_fasta.pl │ └── scripts │ ├── generate_reference.pl │ └── generate_reference_v2.pl ├── 39.housekeepingGeneList ├── HK_genes.txt └── url.lst ├── 40.tm_predictor ├── readme.md ├── tm.matrix └── tm_predictor.pl ├── 41.kaks_calculator ├── 01.run_kaks_calculator.pl ├── 01.run_kaks_calculator.pl.sh ├── 02.collect.pl ├── 02.collect.pl.txt ├── genes │ └── ENSGACP00000000016 │ │ ├── 2NG.dN │ │ ├── 2NG.dS │ │ ├── 2NG.t │ │ ├── 4fold.nuc │ │ ├── branch-site.an.fix.mlc │ │ ├── branch-site.an.nofix.mlc │ │ ├── branch-site.ds.fix.mlc │ │ ├── branch-site.ds.nofix.mlc │ │ ├── branch-site.ss.fix.mlc │ │ ├── branch-site.ss.nofix.mlc │ │ ├── branch.freeratio.mlc │ │ ├── branch.oneratio.mlc │ │ ├── branch.tworatio.an.mlc │ │ ├── branch.tworatio.ds.mlc │ │ ├── branch.tworatio.ss.mlc │ │ ├── cds.fa │ │ ├── cds.log │ │ ├── cds.paml │ │ ├── lnf │ │ ├── rst │ │ ├── rst1 │ │ └── rub └── result │ └── ENSGACP00000000016 │ ├── kaks.ds_gac.axt │ ├── kaks.ds_gac.axt.kaks │ ├── kaks.ds_pol.axt │ ├── kaks.ds_pol.axt.kaks │ ├── kaks.ds_ss.axt │ ├── kaks.ds_ss.axt.kaks │ ├── kaks.ds_tor.axt │ ├── kaks.ds_tor.axt.kaks │ ├── kaks.ss_gac.axt │ ├── kaks.ss_gac.axt.kaks │ ├── kaks.ss_pol.axt │ ├── kaks.ss_pol.axt.kaks │ ├── kaks.ss_tor.axt │ └── kaks.ss_tor.axt.kaks ├── 42.prediction ├── 01.trans_assembly │ ├── 01.run.pl │ ├── 01.run.pl.sh │ ├── 03.predict_cds.pl │ ├── 03.predict_cds.pl.sh │ └── sub.rename.pl ├── 02.protein_align │ ├── 00.protein │ │ └── rename.pl │ └── 01.align │ │ ├── 01.mkdb.pl │ │ ├── 02.query.sh │ │ ├── 03.blat.pl │ │ ├── 04.combine.pl │ │ ├── 05.filter.pl │ │ ├── 06.convert.pl │ │ ├── 07.split_psl.pl │ │ ├── 08.group_species.pl │ │ ├── 09.combine.pl │ │ ├── 10.final_group.pl │ │ ├── 11.filter.pl │ │ └── sub.group_by_species.pl ├── 03.trans_align │ ├── 00.trans │ │ └── 01.collect.sh │ └── 01.align │ │ ├── 02.query.sh │ │ ├── 03.blat.pl │ │ ├── 04.combine_transPSL.pl │ │ ├── 05.filter.pl │ │ ├── 06.convert.pl │ │ ├── 07.split_psl.pl │ │ ├── 08.group_species.pl │ │ ├── 09.combine.pl │ │ ├── 10.final_group.pl │ │ ├── 11.filter.pl │ │ └── sub.group_by_species.pl └── 04.genewise │ ├── 01.prepare.sh │ ├── 02.final_group.pl │ ├── 03.filter.pl │ ├── 04.genewise.pl │ ├── 05.collect.pl │ ├── 06.gff2cds.pl │ ├── result │ └── busco.sh │ ├── sub.convert_genewise.pl │ └── 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