Advanced methods in DNA sequence and multilocus data analyses - MB120P143


Filip Kolář, Tomáš Fér, Pavel Škaloud, Eliška Záveská, Gabriela Šrámková, Jakub Vlček, María Pinilla Vargas, Juan Manuel Gorospe

2023: The course runs on Fridays 9:00-13:00 in Seminarium, Benátská 2, second (uppermost) floor, at the end of corridor at the following dates:

  • 6.10. Lesson 1 - Multilocus data (microsatellites)
  • 20.10. Lesson 2 - Multilocus data (SNPs)
  • 10.11. Lesson 3 - DNA sequences (basic processing)
  • 24.11. Lesson 4 - DNA sequences (multispecies phylogeny reconstructions, molecular dating)
  • 8.12. Lesson 5 - DNA sequences (HybSeq data analysis)
  • 5.1. 2024 Lesson 6 - Integrative analyses

The link to Drive folder with manuals and data and the table listing homework projects are here:

Please install all the programs and packages well on time prior each lesson. We assume Win 10/Linux operation systems. Ask us if you need help before the lesson starts. R program and R studio wrapper will be used throughout. For installing R packages simply use Tools → Install Packages in R Studio or install.packages() function.


Lesson 1

Estimation of population genetic parameters, reconstruction of genetic structure in multilocus data, hybrid detection
programs to install: MSA, R (packages: adegenet, pegas), R studio, Structure, NewHybrids

additional information from a basic course

SNP data

Lesson 2

Structure and population genetic parameters in single nucleotide polymorphism (SNP) data, hierarchical structure in data (AMOVA), geographic covariates of genetic structure

programs to install: R (packages: vcfR, adegenet, adegraphics, pegas, StAMPP, gplots, ggmap), SplitsTree

DNA sequences I

Lesson 3

Sanger sequence and alignment editing, basic single-gene tree construction
programs to install: BioEdit, MEGA, GBlocks, trimAl, jModeltest, RAxML, MrBayes

DNA sequences II

Lesson 4

Species tree reconstruction, networks, incongruence tests, molecular dating
programs to install: SplitsTree, BEAST, PAUP, treePL, RAxML

DNA sequences III - HybSeq

Lesson 5 

Multi-gene species tree reconstruction: tree summary methods (ASTRAL, MRL, FastTree), gene tree incongruence analysis (PhyParts)
programs to install: R (ape, seqinr, data.table), python3, for Microsoft users also enable WSL and install Debian; for the bonus question also install PhyParts (install it under Linux or WSL)

Integrative phylogenetic analyses

Lesson 6

Trait evolution in phylogenetic context, Analysis of complex reticulated phylogenies
programs to install: R (caper, phytools), SplitsTree, PhyloNet, NetRaxML