Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control

The aims of the group MIVEGEC are to develop integrative and transdisciplinary research to the mechanisms that maintain, amplify and transmit pathogenic agents, along with their genetic and epigenetic determinants, in order to better understand how these systems evolve and to improve their control.
L’UMR MIVEGEC "Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle" a pour mission de comprendre, via des recherches intégratives et transdisciplinaires, les mécanismes de maintenance, d’amplification et de transmission d’agents pathogènes, leurs déterminants génétiques et non génétiques, afin de pouvoir mieux appréhender l’évolution de ces systèmes infectieux et contribuer à en améliorer le contrôle.
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121 to 130 of 223 Results
Louis_et_al2023_3.1.2.smartpca_fromhaplo.tar.gz
Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
Gzip Archive - 29.7 MB - MD5: 7f3a8762ab2f1393f629b9061ed84167
CodeData
Scripts and input files to format an haplo file and run smartpca both for the data mapped to the killer whale reference genome and bottlenose dolphin reference genome (see subfolder mapped_Ttruncatus) (Figures 1c, S5 and S6). To uncompress, type "tar xzvf 3.1.2.smartpca_fromhaplo...
Louis_et_al2023_3.2.single_read_PCA.tar.gz
Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
Gzip Archive - 16.2 KB - MD5: 38529e12e86c2043ba0147206cb23475
CodeData
Scripts and input files to run and plot a single-read PCA (Figure S8). To uncompress, type "tar xzvf 3.2.single_read_PCA.tar.gz"
Louis_et_al2023_3.3.tfa.tar.gz
Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
Gzip Archive - 1.1 MB - MD5: 1d4689415c6c66efd15ac30ad8866e16
CodeData
Scripts and input file to run and plot the tfa - factor analysis (Figures 1d and S7). To uncompress, type "tar xzvf 3.3.tfa.tar.gz"
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
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