├── .Rapp.history ├── .gitignore ├── DAF ├── DAFplot.R ├── DeleteriousAlleleFrequency.6.pl ├── README.md ├── combineTwoFiles.R ├── sixPopDAFplot.pdf └── sixPopDAFplot_withoutGuaHigh.pdf ├── Dstatistics ├── 20150707_abba-baba_bathRun.sh ├── Dsummary_0409.pdf ├── Dsummary_0409.txt ├── Dsummary_0409.xlsx ├── Dsummary_0409_Dstatistic.pdf ├── README.md ├── abba-baba.sh ├── angsd.abba-baba.GuaHighvsMexicana.sh ├── angsd.abba-baba.sh ├── jackKnife.R └── resultSummary.txt ├── Figures ├── Figure2Plot.R ├── data │ ├── Figure3.pdf │ ├── MaizePop.homo.GERP0.count.txt │ ├── TeoMaize.fixedSeg.4Sample.100rep.txt │ ├── TeoMaize.homo.GERP0.count.txt │ ├── fd_combine_skinny.txt │ └── sixPop.fixedSeg.3Sample.simplified.txt ├── plotFigure1.R └── plotFigure3.R ├── GATK_SNPcalling ├── README.md ├── command_generator.sh ├── fasta_length.py ├── filterSNP.sub.sbatch ├── filterVCF.sub.sbatch └── vcfsorter.pl ├── GeneticDiversityNeutralTestWithAngsd ├── DerivedHomoSites │ ├── 20150519_derivedHomoSites.sh │ ├── 20150729_derivedHeteroSites.sh │ ├── README.md │ ├── allPop.hetero.counts │ ├── angsd_SNPcall.sh │ ├── numOfDerivedHomoSites.txt │ ├── percDerivedHomo.png │ ├── percHeteroBoxplot.png │ ├── percentOfDerivedHomo.R │ └── percentageOfHeterozygosity.R ├── README.md ├── results │ ├── TajimaD.pdf │ ├── ggplot.boxplot.pi.pdf │ └── ggplot.boxplot.theta.pdf └── scripts │ ├── Angsd.theta.TajimaD.sh │ └── ggplot.boxplot.R ├── NAM.allChr.HMP3.AGPv3.biallele.recode.vcf.gz.tbi ├── NGSadmix ├── README.md ├── results │ ├── NGSadmixK25.jpg │ └── allSamplesK4.png └── scripts │ ├── NGSadmix.plot.R │ ├── allSamples.bamlist │ └── angsd_SNPcall_NGSadmix_allSamples.sh ├── NJtree ├── phangorn_NJtree.R ├── vcf2fasta.sub └── vcf_tab_to_fasta_alignment.pl ├── PCA ├── 20150626PCAwithSNPdataInVCF.sh ├── PCA.ngsCovar.pdf ├── README.md ├── allSamplePCA.eps └── pcaSeeD.png ├── README.md ├── ROH ├── 20150527_plinkROH.sh ├── Ogut2015GeneticMap0.2cMresolution.txt ├── Phys2Genetic_window.R ├── README.md ├── ROH.boxplot.wilcox.test.20150825.R ├── ROH300kb.20snpWindow.1het.hom.simplified ├── ROH300kb.20snpWindow.1het.hom.withCM ├── ROH300kb.20snpWindow.1het.sum.rm1Mb.pdf ├── ROHallSum.pdf ├── ROHbigger1mbSum.pdf ├── ROHcumulativeLength.R ├── ROHless1MbHistogram.pdf └── ROHnewCM2.pdf ├── fd_introgression ├── Angsd_doGeno.sh ├── MexHigh_MexLow_mexicana.bamlist ├── README.md ├── convertDoGeno2egglib.pl ├── doGeno_egglib.sub ├── egglibInput.example.txt ├── egglib_sliding_windows.py ├── fdPlotting.R └── results │ ├── fd.track.allPop.new.pdf │ ├── fd.track.chr3.allPop.span0.01.pdf │ ├── fd.track.chr4.allPop.pdf │ └── fd.track.chr6.allPop.pdf ├── inbreedingCoefficients ├── README.md ├── SWus_indF ├── SWus_samples.txt ├── inbreedingCoefficient.boxplot.R ├── inbreedingCoefficient.boxplot.pdf └── inbreedingCoefficient_ngsF.sh ├── map ├── Genome_Passport_firstVersion_Li.txt ├── distributionMap.R ├── distributionMap.pdf └── distributionMap3.pdf ├── msmc ├── BEAGLEphasing.sh ├── README.md ├── bootstrapMSMC.sub ├── mappabilityMask.pdf ├── maskBed.pipeline.sh ├── msmc.Andes.sub ├── msmcInput.sh └── popSize_plot.py ├── mutationLoad ├── 20160709_gerpLoad_TeoMaize.sh ├── README.md ├── binDerivedAlleleFreq.R ├── derivedAlleleFreq.R ├── genolabs.txt ├── gerpSkinny_derAlleleFreq.txt ├── hm32_skinny.txt └── loadit_LiMod.R ├── serialFounderEffects ├── .Rapp.history ├── 20150521_groupCountryName.sh ├── 23genomeDisHeteroRegression.pdf ├── 31genome.geoDis.hetero.regression.R ├── 31genome.geoDis.perc.hetero.txt ├── 31genome.geoDis.sorted.txt ├── 31genome.geoDis.txt ├── 31genomeDisHeteroRegression.pdf ├── 31genomeDisHeteroRegression.png ├── Fig1C.pdf ├── Fig1C.png ├── Genome_Passport_firstVersion_Li.txt ├── MaizePop.homo.GERP0.count.txt ├── README.md ├── calcPercPolymFromSNPdata.R ├── color.He.from.Balsas.R ├── equation_geoDis_from_longi_latitude.png ├── geoDis.polymorphism.correlation.R ├── geoDisFromLongiLatiDecimal.31genome.py ├── geoDisFromLongiLatiDecimal.py ├── geoDisPolymorphismCorrelation.pdf ├── inbreedingCoefficients.boxplot.pdf ├── perc.hetero.Individual.txt ├── recessiveLoad.distance.pdf ├── recessiveLoad.distance.txt ├── rmMexHighGuaHighCorr.pdf ├── sampleID.gid.location.R └── sampleID.location.geoDis.txt └── trim_mapping_MD ├── 20150709_trim.mapping.MD.sh ├── README.md └── trim_pe.sh /.Rapp.history: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/.gitignore -------------------------------------------------------------------------------- /DAF/DAFplot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/DAF/DAFplot.R -------------------------------------------------------------------------------- /DAF/DeleteriousAlleleFrequency.6.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/DAF/DeleteriousAlleleFrequency.6.pl -------------------------------------------------------------------------------- /DAF/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/DAF/README.md -------------------------------------------------------------------------------- /DAF/combineTwoFiles.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/DAF/combineTwoFiles.R -------------------------------------------------------------------------------- /DAF/sixPopDAFplot.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/DAF/sixPopDAFplot.pdf -------------------------------------------------------------------------------- /DAF/sixPopDAFplot_withoutGuaHigh.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/DAF/sixPopDAFplot_withoutGuaHigh.pdf -------------------------------------------------------------------------------- /Dstatistics/20150707_abba-baba_bathRun.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Dstatistics/20150707_abba-baba_bathRun.sh -------------------------------------------------------------------------------- /Dstatistics/Dsummary_0409.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Dstatistics/Dsummary_0409.pdf -------------------------------------------------------------------------------- /Dstatistics/Dsummary_0409.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Dstatistics/Dsummary_0409.txt -------------------------------------------------------------------------------- /Dstatistics/Dsummary_0409.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Dstatistics/Dsummary_0409.xlsx -------------------------------------------------------------------------------- /Dstatistics/Dsummary_0409_Dstatistic.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Dstatistics/Dsummary_0409_Dstatistic.pdf -------------------------------------------------------------------------------- /Dstatistics/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Dstatistics/README.md -------------------------------------------------------------------------------- /Dstatistics/abba-baba.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Dstatistics/abba-baba.sh -------------------------------------------------------------------------------- /Dstatistics/angsd.abba-baba.GuaHighvsMexicana.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Dstatistics/angsd.abba-baba.GuaHighvsMexicana.sh -------------------------------------------------------------------------------- /Dstatistics/angsd.abba-baba.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Dstatistics/angsd.abba-baba.sh -------------------------------------------------------------------------------- /Dstatistics/jackKnife.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Dstatistics/jackKnife.R -------------------------------------------------------------------------------- /Dstatistics/resultSummary.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Dstatistics/resultSummary.txt -------------------------------------------------------------------------------- /Figures/Figure2Plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Figures/Figure2Plot.R -------------------------------------------------------------------------------- /Figures/data/Figure3.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Figures/data/Figure3.pdf -------------------------------------------------------------------------------- /Figures/data/MaizePop.homo.GERP0.count.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Figures/data/MaizePop.homo.GERP0.count.txt -------------------------------------------------------------------------------- /Figures/data/TeoMaize.fixedSeg.4Sample.100rep.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Figures/data/TeoMaize.fixedSeg.4Sample.100rep.txt -------------------------------------------------------------------------------- /Figures/data/TeoMaize.homo.GERP0.count.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Figures/data/TeoMaize.homo.GERP0.count.txt -------------------------------------------------------------------------------- /Figures/data/fd_combine_skinny.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Figures/data/fd_combine_skinny.txt -------------------------------------------------------------------------------- /Figures/data/sixPop.fixedSeg.3Sample.simplified.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Figures/data/sixPop.fixedSeg.3Sample.simplified.txt -------------------------------------------------------------------------------- /Figures/plotFigure1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Figures/plotFigure1.R -------------------------------------------------------------------------------- /Figures/plotFigure3.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/Figures/plotFigure3.R -------------------------------------------------------------------------------- /GATK_SNPcalling/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GATK_SNPcalling/README.md -------------------------------------------------------------------------------- /GATK_SNPcalling/command_generator.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GATK_SNPcalling/command_generator.sh -------------------------------------------------------------------------------- /GATK_SNPcalling/fasta_length.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GATK_SNPcalling/fasta_length.py -------------------------------------------------------------------------------- /GATK_SNPcalling/filterSNP.sub.sbatch: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GATK_SNPcalling/filterSNP.sub.sbatch -------------------------------------------------------------------------------- /GATK_SNPcalling/filterVCF.sub.sbatch: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GATK_SNPcalling/filterVCF.sub.sbatch -------------------------------------------------------------------------------- /GATK_SNPcalling/vcfsorter.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GATK_SNPcalling/vcfsorter.pl -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/20150519_derivedHomoSites.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/20150519_derivedHomoSites.sh -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/20150729_derivedHeteroSites.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/20150729_derivedHeteroSites.sh -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/README.md -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/allPop.hetero.counts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/allPop.hetero.counts -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/angsd_SNPcall.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/angsd_SNPcall.sh -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/numOfDerivedHomoSites.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/numOfDerivedHomoSites.txt -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/percDerivedHomo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/percDerivedHomo.png -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/percHeteroBoxplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/percHeteroBoxplot.png -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/percentOfDerivedHomo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/percentOfDerivedHomo.R -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/percentageOfHeterozygosity.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/DerivedHomoSites/percentageOfHeterozygosity.R -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/README.md -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/results/TajimaD.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/results/TajimaD.pdf -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/results/ggplot.boxplot.pi.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/results/ggplot.boxplot.pi.pdf -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/results/ggplot.boxplot.theta.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/results/ggplot.boxplot.theta.pdf -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/scripts/Angsd.theta.TajimaD.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/scripts/Angsd.theta.TajimaD.sh -------------------------------------------------------------------------------- /GeneticDiversityNeutralTestWithAngsd/scripts/ggplot.boxplot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/GeneticDiversityNeutralTestWithAngsd/scripts/ggplot.boxplot.R -------------------------------------------------------------------------------- /NAM.allChr.HMP3.AGPv3.biallele.recode.vcf.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/NAM.allChr.HMP3.AGPv3.biallele.recode.vcf.gz.tbi -------------------------------------------------------------------------------- /NGSadmix/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/NGSadmix/README.md -------------------------------------------------------------------------------- /NGSadmix/results/NGSadmixK25.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/NGSadmix/results/NGSadmixK25.jpg -------------------------------------------------------------------------------- /NGSadmix/results/allSamplesK4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/NGSadmix/results/allSamplesK4.png -------------------------------------------------------------------------------- /NGSadmix/scripts/NGSadmix.plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/NGSadmix/scripts/NGSadmix.plot.R -------------------------------------------------------------------------------- /NGSadmix/scripts/allSamples.bamlist: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/NGSadmix/scripts/allSamples.bamlist -------------------------------------------------------------------------------- /NGSadmix/scripts/angsd_SNPcall_NGSadmix_allSamples.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/NGSadmix/scripts/angsd_SNPcall_NGSadmix_allSamples.sh -------------------------------------------------------------------------------- /NJtree/phangorn_NJtree.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/NJtree/phangorn_NJtree.R -------------------------------------------------------------------------------- /NJtree/vcf2fasta.sub: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/NJtree/vcf2fasta.sub -------------------------------------------------------------------------------- /NJtree/vcf_tab_to_fasta_alignment.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/NJtree/vcf_tab_to_fasta_alignment.pl -------------------------------------------------------------------------------- /PCA/20150626PCAwithSNPdataInVCF.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/PCA/20150626PCAwithSNPdataInVCF.sh -------------------------------------------------------------------------------- /PCA/PCA.ngsCovar.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/PCA/PCA.ngsCovar.pdf -------------------------------------------------------------------------------- /PCA/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/PCA/README.md -------------------------------------------------------------------------------- /PCA/allSamplePCA.eps: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/PCA/allSamplePCA.eps -------------------------------------------------------------------------------- /PCA/pcaSeeD.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/PCA/pcaSeeD.png -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/README.md -------------------------------------------------------------------------------- /ROH/20150527_plinkROH.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/ROH/20150527_plinkROH.sh -------------------------------------------------------------------------------- /ROH/Ogut2015GeneticMap0.2cMresolution.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/ROH/Ogut2015GeneticMap0.2cMresolution.txt -------------------------------------------------------------------------------- /ROH/Phys2Genetic_window.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/ROH/Phys2Genetic_window.R -------------------------------------------------------------------------------- /ROH/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/ROH/README.md -------------------------------------------------------------------------------- /ROH/ROH.boxplot.wilcox.test.20150825.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/ROH/ROH.boxplot.wilcox.test.20150825.R -------------------------------------------------------------------------------- /ROH/ROH300kb.20snpWindow.1het.hom.simplified: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/ROH/ROH300kb.20snpWindow.1het.hom.simplified -------------------------------------------------------------------------------- /ROH/ROH300kb.20snpWindow.1het.hom.withCM: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/ROH/ROH300kb.20snpWindow.1het.hom.withCM -------------------------------------------------------------------------------- /ROH/ROH300kb.20snpWindow.1het.sum.rm1Mb.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/ROH/ROH300kb.20snpWindow.1het.sum.rm1Mb.pdf -------------------------------------------------------------------------------- /ROH/ROHallSum.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/ROH/ROHallSum.pdf -------------------------------------------------------------------------------- /ROH/ROHbigger1mbSum.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/ROH/ROHbigger1mbSum.pdf -------------------------------------------------------------------------------- /ROH/ROHcumulativeLength.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/ROH/ROHcumulativeLength.R -------------------------------------------------------------------------------- /ROH/ROHless1MbHistogram.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/ROH/ROHless1MbHistogram.pdf -------------------------------------------------------------------------------- /ROH/ROHnewCM2.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/ROH/ROHnewCM2.pdf -------------------------------------------------------------------------------- /fd_introgression/Angsd_doGeno.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/fd_introgression/Angsd_doGeno.sh -------------------------------------------------------------------------------- /fd_introgression/MexHigh_MexLow_mexicana.bamlist: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/fd_introgression/MexHigh_MexLow_mexicana.bamlist -------------------------------------------------------------------------------- /fd_introgression/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/fd_introgression/README.md -------------------------------------------------------------------------------- /fd_introgression/convertDoGeno2egglib.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/fd_introgression/convertDoGeno2egglib.pl -------------------------------------------------------------------------------- /fd_introgression/doGeno_egglib.sub: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/fd_introgression/doGeno_egglib.sub -------------------------------------------------------------------------------- /fd_introgression/egglibInput.example.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/fd_introgression/egglibInput.example.txt -------------------------------------------------------------------------------- /fd_introgression/egglib_sliding_windows.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/fd_introgression/egglib_sliding_windows.py -------------------------------------------------------------------------------- /fd_introgression/fdPlotting.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/fd_introgression/fdPlotting.R -------------------------------------------------------------------------------- /fd_introgression/results/fd.track.allPop.new.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/fd_introgression/results/fd.track.allPop.new.pdf -------------------------------------------------------------------------------- /fd_introgression/results/fd.track.chr3.allPop.span0.01.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/fd_introgression/results/fd.track.chr3.allPop.span0.01.pdf -------------------------------------------------------------------------------- /fd_introgression/results/fd.track.chr4.allPop.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/fd_introgression/results/fd.track.chr4.allPop.pdf -------------------------------------------------------------------------------- /fd_introgression/results/fd.track.chr6.allPop.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/fd_introgression/results/fd.track.chr6.allPop.pdf -------------------------------------------------------------------------------- /inbreedingCoefficients/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/inbreedingCoefficients/README.md -------------------------------------------------------------------------------- /inbreedingCoefficients/SWus_indF: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/inbreedingCoefficients/SWus_indF -------------------------------------------------------------------------------- /inbreedingCoefficients/SWus_samples.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/inbreedingCoefficients/SWus_samples.txt -------------------------------------------------------------------------------- /inbreedingCoefficients/inbreedingCoefficient.boxplot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/inbreedingCoefficients/inbreedingCoefficient.boxplot.R -------------------------------------------------------------------------------- /inbreedingCoefficients/inbreedingCoefficient.boxplot.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/inbreedingCoefficients/inbreedingCoefficient.boxplot.pdf -------------------------------------------------------------------------------- /inbreedingCoefficients/inbreedingCoefficient_ngsF.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/inbreedingCoefficients/inbreedingCoefficient_ngsF.sh -------------------------------------------------------------------------------- /map/Genome_Passport_firstVersion_Li.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/map/Genome_Passport_firstVersion_Li.txt -------------------------------------------------------------------------------- /map/distributionMap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/map/distributionMap.R -------------------------------------------------------------------------------- /map/distributionMap.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/map/distributionMap.pdf -------------------------------------------------------------------------------- /map/distributionMap3.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/map/distributionMap3.pdf -------------------------------------------------------------------------------- /msmc/BEAGLEphasing.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/msmc/BEAGLEphasing.sh -------------------------------------------------------------------------------- /msmc/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/msmc/README.md -------------------------------------------------------------------------------- /msmc/bootstrapMSMC.sub: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/msmc/bootstrapMSMC.sub -------------------------------------------------------------------------------- /msmc/mappabilityMask.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/msmc/mappabilityMask.pdf -------------------------------------------------------------------------------- /msmc/maskBed.pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/msmc/maskBed.pipeline.sh -------------------------------------------------------------------------------- /msmc/msmc.Andes.sub: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/msmc/msmc.Andes.sub -------------------------------------------------------------------------------- /msmc/msmcInput.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/msmc/msmcInput.sh -------------------------------------------------------------------------------- /msmc/popSize_plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/msmc/popSize_plot.py -------------------------------------------------------------------------------- /mutationLoad/20160709_gerpLoad_TeoMaize.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/mutationLoad/20160709_gerpLoad_TeoMaize.sh -------------------------------------------------------------------------------- /mutationLoad/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/mutationLoad/README.md -------------------------------------------------------------------------------- /mutationLoad/binDerivedAlleleFreq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/mutationLoad/binDerivedAlleleFreq.R -------------------------------------------------------------------------------- /mutationLoad/derivedAlleleFreq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/mutationLoad/derivedAlleleFreq.R -------------------------------------------------------------------------------- /mutationLoad/genolabs.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/mutationLoad/genolabs.txt -------------------------------------------------------------------------------- /mutationLoad/gerpSkinny_derAlleleFreq.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/mutationLoad/gerpSkinny_derAlleleFreq.txt -------------------------------------------------------------------------------- /mutationLoad/hm32_skinny.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/mutationLoad/hm32_skinny.txt -------------------------------------------------------------------------------- /mutationLoad/loadit_LiMod.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/mutationLoad/loadit_LiMod.R -------------------------------------------------------------------------------- /serialFounderEffects/.Rapp.history: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /serialFounderEffects/20150521_groupCountryName.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/20150521_groupCountryName.sh -------------------------------------------------------------------------------- /serialFounderEffects/23genomeDisHeteroRegression.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/23genomeDisHeteroRegression.pdf -------------------------------------------------------------------------------- /serialFounderEffects/31genome.geoDis.hetero.regression.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/31genome.geoDis.hetero.regression.R -------------------------------------------------------------------------------- /serialFounderEffects/31genome.geoDis.perc.hetero.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/31genome.geoDis.perc.hetero.txt -------------------------------------------------------------------------------- /serialFounderEffects/31genome.geoDis.sorted.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/31genome.geoDis.sorted.txt -------------------------------------------------------------------------------- /serialFounderEffects/31genome.geoDis.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/31genome.geoDis.txt -------------------------------------------------------------------------------- /serialFounderEffects/31genomeDisHeteroRegression.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/31genomeDisHeteroRegression.pdf -------------------------------------------------------------------------------- /serialFounderEffects/31genomeDisHeteroRegression.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/31genomeDisHeteroRegression.png -------------------------------------------------------------------------------- /serialFounderEffects/Fig1C.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/Fig1C.pdf -------------------------------------------------------------------------------- /serialFounderEffects/Fig1C.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/Fig1C.png -------------------------------------------------------------------------------- /serialFounderEffects/Genome_Passport_firstVersion_Li.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/Genome_Passport_firstVersion_Li.txt -------------------------------------------------------------------------------- /serialFounderEffects/MaizePop.homo.GERP0.count.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/MaizePop.homo.GERP0.count.txt -------------------------------------------------------------------------------- /serialFounderEffects/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/README.md -------------------------------------------------------------------------------- /serialFounderEffects/calcPercPolymFromSNPdata.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/calcPercPolymFromSNPdata.R -------------------------------------------------------------------------------- /serialFounderEffects/color.He.from.Balsas.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/color.He.from.Balsas.R -------------------------------------------------------------------------------- /serialFounderEffects/equation_geoDis_from_longi_latitude.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/equation_geoDis_from_longi_latitude.png -------------------------------------------------------------------------------- /serialFounderEffects/geoDis.polymorphism.correlation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/geoDis.polymorphism.correlation.R -------------------------------------------------------------------------------- /serialFounderEffects/geoDisFromLongiLatiDecimal.31genome.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/geoDisFromLongiLatiDecimal.31genome.py -------------------------------------------------------------------------------- /serialFounderEffects/geoDisFromLongiLatiDecimal.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/geoDisFromLongiLatiDecimal.py -------------------------------------------------------------------------------- /serialFounderEffects/geoDisPolymorphismCorrelation.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/geoDisPolymorphismCorrelation.pdf -------------------------------------------------------------------------------- /serialFounderEffects/inbreedingCoefficients.boxplot.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/inbreedingCoefficients.boxplot.pdf -------------------------------------------------------------------------------- /serialFounderEffects/perc.hetero.Individual.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/perc.hetero.Individual.txt -------------------------------------------------------------------------------- /serialFounderEffects/recessiveLoad.distance.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/recessiveLoad.distance.pdf -------------------------------------------------------------------------------- /serialFounderEffects/recessiveLoad.distance.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/recessiveLoad.distance.txt -------------------------------------------------------------------------------- /serialFounderEffects/rmMexHighGuaHighCorr.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/rmMexHighGuaHighCorr.pdf -------------------------------------------------------------------------------- /serialFounderEffects/sampleID.gid.location.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/sampleID.gid.location.R -------------------------------------------------------------------------------- /serialFounderEffects/sampleID.location.geoDis.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/serialFounderEffects/sampleID.location.geoDis.txt -------------------------------------------------------------------------------- /trim_mapping_MD/20150709_trim.mapping.MD.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/trim_mapping_MD/20150709_trim.mapping.MD.sh -------------------------------------------------------------------------------- /trim_mapping_MD/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/trim_mapping_MD/README.md -------------------------------------------------------------------------------- /trim_mapping_MD/trim_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HuffordLab/Wang_et_al._Demography/HEAD/trim_mapping_MD/trim_pe.sh --------------------------------------------------------------------------------