├── README.md ├── demographic-analysis ├── PSMC │ └── run.sh └── SMC++ │ ├── 1get_vcf.sh │ ├── 2mask.sh │ ├── 3sample.R │ ├── 4vcf2smc_ind1.sh │ ├── 5estimate_ind1.sh │ └── 6plot.sh ├── gene-flow ├── data_file_link ├── niv2_f3.sh ├── niv2_f3_list ├── niv2_f3_parfile ├── niv2_qpDstat.sh ├── niv2_qpDstat_list └── niv2_qpDstat_parfile ├── haplotypic-analysis ├── 201110.sample.grp ├── div │ ├── Os01g0259900.1k.pi.filter │ ├── Os01g0259900.filter.segment.pi │ └── Os01g0259900.segment.pi ├── nsg │ ├── Os01g0259900.1k.pi.filter │ ├── Os01g0259900.sample.missing │ └── Os01g0259900.segment.vcf.gz ├── phs │ ├── Os01g0259900.hap.vcf.gz │ └── Os01g0259900.segment.gt.vcf.gz ├── seg │ └── Os01g0259900.segment.vcf.gz ├── sta │ └── Os01g0259900.hap.sta ├── step1-build.snp.pos.index.pl ├── step2-get.target.segment.vcf.pl ├── step3-cal.site.diversity.and.filtering.pl ├── step4-filter.sample.pl ├── step5-phasing.gene.segment.pl ├── step6-sta.for.hap.pl └── target.gene.list ├── mapping-and-variant-discovery ├── construct_knowsite.sh ├── mapping_short_reads.sh └── variant_discovery_and_filtering.sh ├── phylogenetic-analysis ├── build.fr.idx.pl ├── cal.pop.fr.pl ├── cal.pop.parameter.pl ├── cal.pop.tree.pl ├── cal_bootstrip.pl └── phylogenetic-analysis.sh ├── population-genetic-analysis ├── Population_PopLDdecay.sh └── Population_genetic_analysis.sh └── selective-sweep-and-gene-identification ├── step1.cal.fr.pl ├── step2.build.pos.idx.pl ├── step3a.cal.gene.pl └── step3b.cal.sw.pl /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zhangfumin/domestication/HEAD/README.md -------------------------------------------------------------------------------- /demographic-analysis/PSMC/run.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zhangfumin/domestication/HEAD/demographic-analysis/PSMC/run.sh 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