Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles

Pipeline used in:

J.L. Leal, Pascal Milesi, Eva Hodková, Qiujie Zhou, Jennifer James, D. Magnus Eklund, Tanja Pyhäjärvi, Jarkko Salojärvi, and Martin Lascoux

Systematic Biology (2024) doi: 10.1093/sysbio/syae012

Name		Name	Last commit message	Last commit date
Latest commit History 188 Commits
01_Read_mapping_and_variant_calling		01_Read_mapping_and_variant_calling
02_Classification_of_polyploid_specimens		02_Classification_of_polyploid_specimens
03_Generate_MSAs		03_Generate_MSAs
04_Polarize_polyploid		04_Polarize_polyploid
05_Phylogenetic_Analysis		05_Phylogenetic_Analysis
06_Prepare_data_for_STRUCTURE_and_adegenet_analyses		06_Prepare_data_for_STRUCTURE_and_adegenet_analyses
07_STRUCTURE_analysis		07_STRUCTURE_analysis
08_DAPC_adegenet		08_DAPC_adegenet
09_Model_Testing_1_Polyploidization_and_hybridization_simulations		09_Model_Testing_1_Polyploidization_and_hybridization_simulations
10_Model_Testing_2_Model_evaluation		10_Model_Testing_2_Model_evaluation
11_Demographic_modeling		11_Demographic_modeling
12_nana_humilis_alleles_geographic_distribution		12_nana_humilis_alleles_geographic_distribution
README.md		README.md