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] February 8 to 11, 2021 . Vojtěch Zeisek (https://trapa.cz/) Molecular data in R February 8 to 11, 2021 1 / 421 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 Tasks Packages for our work 3 Data Overview of data and data types Microsatellites AFLP Notes about data DNA sequences, SNP . VCF . Vojtěch Zeisek (https://trapa.cz/) Molecular data in R February 8 to 11, 2021 2 / 421 Introduction R Data Alignment Basic analysis SNP DAPC Structure Spatial analysis Trees Evolution The end Outline II Export Tasks 4 Alignment Overview and MAFFT MAFFT, Clustal, MUSCLE and T-Coffee Multiple genes Display and cleaning Tasks 5 Basic analysis First look at the data Statistics MSN . Genetic distances . Vojtěch Zeisek (https://trapa.cz/) Molecular data in R February 8 to 11, 2021 3 / 421 Introduction R Data Alignment Basic analysis SNP DAPC Structure Spatial analysis Trees Evolution The end Outline III AMOVA Hierarchical clustering NJ (and UPGMA) tree PCoA Tasks 6 SNP PCA and NJ 7 DAPC Bayesian clustering Discriminant analysis and visualization Tasks 8 Structure Running Structure from R . Vojtěch Zeisek (https://trapa.cz/) Molecular data in R February 8 to 11, 2021 4 / 421 Introduction R Data Alignment Basic analysis SNP DAPC Structure Spatial analysis Trees Evolution The end Outline IV ParallelStructure on Windows Post processing 9 Spatial analysis Moran’s I sPCA Monmonier Mantel test Geneland Plotting maps Tasks 10 Trees Manipulations .