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Publication Year: 2023

471 to 480 of 697 Results

Louis_et_al2023_3.4.PCA_downsampling_modern.tar.gz Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Gzip Archive - 13.1 MB - MD5: 39d6bc3f6db277efe72dc0fb0dd72e8d CodeData Scripts and input files to run smartpca (subfolder 3.4.1.smartpca) and the single read PCA (subfolder 3.4.2.single_read) on the modern data including one individual downsampled to 0.03x (Figure S3). To uncompress, type "tar xzvf 3.4.PCA_downsampling_modern.tar.gz"
Louis_et_al2023_4.1.D_statistics.tar.gz Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Gzip Archive - 12.8 KB - MD5: 068eb49f9c9aaeb60632c4cde49783ca CodeData Scripts and input files to run D-statistics (Figures S9 and S10). To uncompress, type "tar xzvf 4.1.D_statistics.tar.gz"
Louis_et_al2023_4.2.qpbrute.tar.gz Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Gzip Archive - 21.9 MB - MD5: 823c1555aa862779e58967acee925a6c CodeData Scripts and input file to format the files and run qprbute from an haplo file (subfolder 4.2.1.pseudohaploid_withSP1060) or a vcf file (subfolder 4.2.2.genotypes_modern) (Figure 2 and S11). To uncompress, type "tar xzvf 4.2.qpbrute.tar.gz"
Louis_et_al2023_5.selection.tar.gz Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Gzip Archive - 7.8 MB - MD5: 19899db3c096b4cc9e222b9477f727ea CodeData Scripts and input files to run and plot heterozygosity (subfolder 5.1.heterozygosity), and genotype plots, NJ tree (including bootstrapping) and PCA (subfolder P5.2.CA_NJtree_genotype_plot) for the SNPs under parallel linked selection. There is aslo a subfolder within 5.2. to gen...
Louis_et_al2023_6.mitogenomes.tar.gz Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Gzip Archive - 299.5 KB - MD5: a870965b07accdc346cfbb09c65b1a7d CodeData Scripts and input files to generate the mitogenone analyses (Figure S1). R script and files to plot the samples (Figure 1a). To uncompress, type "tar xzvf 6.mitogenomes.tar.gz"
Louis_et_al2023_code_data_analyses.txt Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Plain Text - 45.4 KB - MD5: 7bb222a264abcc01418451e30dfaf646 CodeDocumentation Scripts, tools, and data to reproduce all the analyses in the manuscript
Louis_et_al2023_code_mapping_filtering_ancientDNA.txt Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Plain Text - 42.3 KB - MD5: 9a5937cb6042ca80fad874efed927c35 CodeDocumentation Pipeline (in shell) to map and filter the ancient DNA data
Louis_et_al2023_code_mapping_filtering_contemporaryDNA.txt Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Plain Text - 29.3 KB - MD5: 55ba283fcdd3d70e06bbfcd0c109b3e4 CodeDocumentation Pipeline (in shell) to map and filter the contemporary DNA data, including the three new samples, and the outgroups (killer whale and Indo-Pacific bottlenose dolphin)
Louis_et_al2023_map.tar.gz Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Gzip Archive - 299.5 KB - MD5: 92824da49b11ec507505443c62440966 CodeData R script and files to plot the samples (Figure 1a). To uncompress, type "tar xzvf map.tar.gz"
Louis_et_al2023_Readme.txt Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Plain Text - 3.2 KB - MD5: 7d092982e6c3423f1f2d6efdfa6941a3 Documentation README file detailing the content of each file and folder

Louis_et_al2023_3.4.PCA_downsampling_modern.tar.gz

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Gzip Archive - 13.1 MB -

CodeData

Scripts and input files to run smartpca (subfolder 3.4.1.smartpca) and the single read PCA (subfolder 3.4.2.single_read) on the modern data including one individual downsampled to 0.03x (Figure S3). To uncompress, type "tar xzvf 3.4.PCA_downsampling_modern.tar.gz"

Louis_et_al2023_4.1.D_statistics.tar.gz

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Gzip Archive - 12.8 KB -

CodeData

Scripts and input files to run D-statistics (Figures S9 and S10). To uncompress, type "tar xzvf 4.1.D_statistics.tar.gz"

Louis_et_al2023_4.2.qpbrute.tar.gz

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Gzip Archive - 21.9 MB -

CodeData

Scripts and input file to format the files and run qprbute from an haplo file (subfolder 4.2.1.pseudohaploid_withSP1060) or a vcf file (subfolder 4.2.2.genotypes_modern) (Figure 2 and S11). To uncompress, type "tar xzvf 4.2.qpbrute.tar.gz"

Louis_et_al2023_5.selection.tar.gz

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Gzip Archive - 7.8 MB -

CodeData

Scripts and input files to run and plot heterozygosity (subfolder 5.1.heterozygosity), and genotype plots, NJ tree (including bootstrapping) and PCA (subfolder P5.2.CA_NJtree_genotype_plot) for the SNPs under parallel linked selection. There is aslo a subfolder within 5.2. to gen...

Louis_et_al2023_6.mitogenomes.tar.gz

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Gzip Archive - 299.5 KB -

CodeData

Scripts and input files to generate the mitogenone analyses (Figure S1). R script and files to plot the samples (Figure 1a). To uncompress, type "tar xzvf 6.mitogenomes.tar.gz"

Louis_et_al2023_code_data_analyses.txt

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Plain Text - 45.4 KB -

CodeDocumentation

Scripts, tools, and data to reproduce all the analyses in the manuscript

Louis_et_al2023_code_mapping_filtering_ancientDNA.txt

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Plain Text - 42.3 KB -

CodeDocumentation

Pipeline (in shell) to map and filter the ancient DNA data

Louis_et_al2023_code_mapping_filtering_contemporaryDNA.txt

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Plain Text - 29.3 KB -

CodeDocumentation

Pipeline (in shell) to map and filter the contemporary DNA data, including the three new samples, and the outgroups (killer whale and Indo-Pacific bottlenose dolphin)

Louis_et_al2023_map.tar.gz

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Gzip Archive - 299.5 KB -

CodeData

R script and files to plot the samples (Figure 1a). To uncompress, type "tar xzvf map.tar.gz"

Louis_et_al2023_Readme.txt

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Plain Text - 3.2 KB -

Documentation

README file detailing the content of each file and folder

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