Introduction R Data Alignment Basic analysis SNP DAPC Structure Spatial analysis Trees Evolution The end Molecular data in R Phylogeny, evolution & R Vojtěch Zeisek Department of Botany, Faculty of Science, Charles University, Prague Institute of Botany, Czech Academy of Sciences, Průhonice https://trapa.cz/,
[email protected] January 27 to 30, 2020 . Vojtěch Zeisek (https://trapa.cz/) Molecular data in R January 27 to 30, 2020 1 / 393 Introduction R Data Alignment Basic analysis SNP DAPC Structure Spatial analysis Trees Evolution The end Outline I 1 Introduction 2 R Installation Let’s start with R Basic operations in R Packages for our work 3 Data Overview of data and data types Microsatellites AFLP Notes about data DNA sequences, SNP VCF Export . Vojtěch Zeisek (https://trapa.cz/) Molecular data in R January 27 to 30, 2020 2 / 393 Introduction R Data Alignment Basic analysis SNP DAPC Structure Spatial analysis Trees Evolution The end Outline II Tasks 4 Alignment Overview and MAFFT MAFFT, Clustal, MUSCLE and T-Coffee Multiple genes Display and cleaning 5 Basic analysis First look at the data Statistics Genetic distances Hierarchical clustering AMOVA . MSN . Vojtěch Zeisek (https://trapa.cz/) Molecular data in R January 27 to 30, 2020 3 / 393 Introduction R Data Alignment Basic analysis SNP DAPC Structure Spatial analysis Trees Evolution The end Outline III NJ (and UPGMA) tree PCoA Tasks 6 SNP PCA and NJ 7 DAPC Bayesian clustering Discriminant analysis and visualization 8 Structure Running Structure from R ParallelStructure on Windows Post processing 9 Spatial analysis . Vojtěch Zeisek (https://trapa.cz/) Molecular data in R January 27 to 30, 2020 4 / 393 Introduction R Data Alignment Basic analysis SNP DAPC Structure Spatial analysis Trees Evolution The end Outline IV Moran’s I sPCA Monmonier Mantel test Geneland Plotting maps 10 Trees Manipulations MP Seeing trees in the forest Comparisons Notes about plotting the trees .