├── 1. Read alignment, SNP and genotype calling ├── 1-runBWA_mem.sh ├── 2-realign.sh ├── 3-picard_markduplicates.sh ├── 4-haplotypecaller.sh ├── 5-genotypeGVCFs.sh ├── 6-vcf_geno_dep.filtering.4species.sh └── README ├── 2. Phylogenetic relationships and population structure analysis ├── 1-UnifiedGenotyper.chloroplast.sh ├── 2-chloroplast_vcf_filtering.sh ├── 3-SNPhylo-chloroplast.sh ├── 4-SNPhylo-chloroplast.tree.R ├── 5-angsd_PCA.4species.sh ├── 6-pca.plot.R ├── 7-beagle_phasing.sh ├── 8-beagle_ibd.plot.R └── README ├── 3. Demographic history reconstruction ├── README ├── fastsimcal │ ├── 1-angsd_2dsfs.chr.sh │ ├── 2-angsd_2dsfs.matrix.R │ ├── 3-aspen.3species.model26.sh │ ├── 4-model26_bootstrap.sh │ └── README └── msmc │ ├── 1-msmc2.4species.input.sh │ ├── 2-msmc2.4species.run.sh │ ├── 3-msmc2.4species.submit.sh │ ├── 4-msmc2.4species.results_merge.sh │ ├── 5-msmc2.plot.R │ └── README ├── 4. Intra- and inter- species summary statistics ├── 1-angsd_SFS_davidiana.sh ├── 1-angsd_SFS_tremula.sh ├── 1-angsd_SFS_tremuloides.sh ├── 1-angsd_SFS_trichocarpa.sh ├── 2-thetas_table.R ├── 3-angsd_FST.6species_pair.sh ├── 4-angsd_dxy.6species_pair.sh ├── 5-angsd_fst_stat_win.noChr.R ├── 5-fst.dxy.6species_pair.sh ├── 6-ldhelmet.4species.sh ├── 6-ldhelmet.window.summary.R ├── 7-Figure2_diversity_divergence_rho.4species.100kb.R ├── 7-diversity_divergence_rho.4species.10kb.R ├── 8-linked_selection.correlation.R ├── 9-Figure4.R └── README ├── 5-phylogenomic_introgression_analyses ├── 1-twisst.ABBABABA.sh ├── 2-ILS.allele_freq.sh ├── 3-ILS_gene.sh ├── 3-vcf2bed.awk ├── 4-ILS.R ├── 5-Figure3_FigureS10S11.R ├── 6-angsd_abbababa2.sh └── README ├── 6-positive_balancing_selection ├── 1-Figure5.R ├── 1-interpolate_map_to_snp.R ├── 1-manhanttan_plot.R ├── 1-xpclr.aspen_species.rec_cM.sh ├── 1-xpclr_convert_rho_to_cM.R ├── 2-Figure6.R ├── 2-betascan.sh └── README └── README.md /1. 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