Origin and fate of supergenes in Atlantic cod
Creators
- 1. Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
- 2. Zoological Institute, University of Basel, Basel, Switzerland
- 3. Marine and Freshwater Research Institute, Hafnarfjördur, Iceland
- 4. Ian
- 5. Kjetill Sigurd
- 6. Sissel
Description
Input and output files for analyses of divergence times of Gadinae with StarBEAST2
gadinae_starbeast_alignments.tgz
gadinae_starbeast.xml
gadinae_starbeast.log
gadinae_starbeast.trees
gadinae_starbeast.tre
Input and output files for analyses of divergence times and introgression among Gadus, Arctogadus, and Boreogadus with AIM
gadus_arctogadus_boreogadus_aim_alignments.tgz
gadus_arctogadus_boreogadus_aim.xml
gadus_arctogadus_boreogadus_aim.log
gadus_arctogadus_boreogadus_aim.trees
gadus_arctogadus_boreogadus_aim_bpp0763.tre
gadus_arctogadus_boreogadus_aim_bpp0234.tre
Dataset used for analyses of introgression among Gadus, Arctogadus, and Boreogadus with Dsuite
gadus_arctogadus_boreogadus_dsuite.vcf.gz
Alignments and output trees for analyses of tree-based signals of introgression among Gadus, Arctogadus, and Boreogadus with IQ-TREE
gadus_arctogadus_boreogadus_iqtree_alignments.tgz
gadus_arctogadus_boreogadus_iqtree_trees.tgz
Datasets used for supergene-specific analyses of linkage disequilibrium in Gadus morhua with PLINK
gadus_morhua_supergene_lg01_plink.map
gadus_morhua_supergene_lg01_plink.ped
gadus_morhua_supergene_lg02_plink.map
gadus_morhua_supergene_lg02_plink.ped
gadus_morhua_supergene_lg07_plink.map
gadus_morhua_supergene_lg07_plink.ped
gadus_morhua_supergene_lg12_plink.map
gadus_morhua_supergene_lg12_plink.ped
Input and output files for analyses of divergence times among Gadus morhua populations with SNAPP
gadus_morhua_outside_supergenes_snapp.vcf.gz
gadus_morhua_outside_supergenes_snapp.xml
gadus_morhua_outside_supergenes_snapp.log
gadus_morhua_outside_supergenes_snapp.tre
gadus_morhua_outside_supergenes_snapp.trees
Dataset used for analyses of introgression among Gadus morhua populations with Dsuite
gadus_morhua_outside_supergenes_dsuite.vcf.gz
Dataset used for analyses of demograpy of Gadus morhua populations with Relate
gadus_morhua_outside_supergenes_relate.vcf.gz
Input and output files for supergene-specific analyses of divergence times among Gadus morhua populations with SNAPP
gadus_morhua_supergene_lg01_snapp.vcf.gz
gadus_morhua_supergene_lg01_snapp.xml
gadus_morhua_supergene_lg01_snapp.log
gadus_morhua_supergene_lg01_snapp.trees
gadus_morhua_supergene_lg01_snapp.tre
gadus_morhua_supergene_lg02_snapp.vcf.gz
gadus_morhua_supergene_lg02_snapp.xml
gadus_morhua_supergene_lg02_snapp.log
gadus_morhua_supergene_lg02_snapp.trees
gadus_morhua_supergene_lg02_snapp.tre
gadus_morhua_supergene_lg07_snapp.vcf.gz
gadus_morhua_supergene_lg07_snapp.xml
gadus_morhua_supergene_lg07_snapp.log
gadus_morhua_supergene_lg07_snapp.trees
gadus_morhua_supergene_lg07_snapp.tre
gadus_morhua_supergene_lg12_snapp.vcf.gz
gadus_morhua_supergene_lg12_snapp.xml
gadus_morhua_supergene_lg12_snapp.log
gadus_morhua_supergene_lg12_snapp.trees
gadus_morhua_supergene_lg12_snapp.tre
Datasets used for supergene-specific analyses of introgression among Gadus morhua populations with Dsuite
gadus_morhua_supergene_lg01_dsuite.vcf.gz
gadus_morhua_supergene_lg02_dsuite.vcf.gz
gadus_morhua_supergene_lg07_dsuite.vcf.gz
gadus_morhua_supergene_lg12_dsuite.vcf.gz
Datasets used for supergene-specific analyses of demograpy of Gadus morhua populations with Relate
gadus_morhua_supergene_lg01_relate.vcf.gz
gadus_morhua_supergene_lg02_relate.vcf.gz
gadus_morhua_supergene_lg07_relate.vcf.gz
gadus_morhua_supergene_lg12_relate.vcf.gz
Files
gadinae_starbeast.xml
Files
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