population_genomics_climate_adaptation_scripts

Scripts used in MBE paper for population genomics analysis of Thrips palmi.

Name		Name	Last commit message	Last commit date
Latest commit History 4 Commits
01_fastp.pl		01_fastp.pl
02_2mapping_mutisamples.pl		02_2mapping_mutisamples.pl
02_3call_snp.pl		02_3call_snp.pl
02_4joinGVCFS_by_chr.pl		02_4joinGVCFS_by_chr.pl
02_5gather_cmd.sh		02_5gather_cmd.sh
02_getNM.pl		02_getNM.pl
02_pick.coverage.pl		02_pick.coverage.pl
02_pick_up_mapping_quality.pl		02_pick_up_mapping_quality.pl
03_missing_persample.R		03_missing_persample.R
03_vcf_filter.sh		03_vcf_filter.sh
04_pixy_pi.sh		04_pixy_pi.sh
04_populations.sh		04_populations.sh
05_admixture.sh		05_admixture.sh
05_distruct2.2_ocwa.py		05_distruct2.2_ocwa.py
05_pca.R		05_pca.R
06_optM.R		06_optM.R
06_treemix.sh		06_treemix.sh
07_KimTree.R		07_KimTree.R
07_kimtree.sh		07_kimtree.sh
07_kimtreeResults.R		07_kimtreeResults.R
08. SMC++.sh		08. SMC++.sh
09. plot_vcfdecay_from_vcf.sh		09. plot_vcfdecay_from_vcf.sh
09. splitPop.sh		09. splitPop.sh
10. pixy--fst.sh		10. pixy--fst.sh
10. vcftools-fst.sh		10. vcftools-fst.sh
11. pixy--dxy.sh		11. pixy--dxy.sh
12. IBD.R		12. IBD.R
13. 00_rda.sh		13. 00_rda.sh
13. 01_PCs_4fds.R		13. 01_PCs_4fds.R
13. 02rda_tp_16pops.R		13. 02rda_tp_16pops.R
13. rdadapt.R		13. rdadapt.R
14. 16pops_lfmm2.R		14. 16pops_lfmm2.R
15.gfScripts_outlier_data.R		15.gfScripts_outlier_data.R
16. tp_kegg.go.R		16. tp_kegg.go.R
17. localPCA1_LD_calculate.sh		17. localPCA1_LD_calculate.sh
17. localPCA3_plot_LD_matrix.R		17. localPCA3_plot_LD_matrix.R
README.md		README.md
localPCA1_lostruct.R		localPCA1_lostruct.R

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