Advanced methods in DNA sequence and mulilocus data analyses - MB120P143

Lecturers: Filip Kolář, Tomáš Fér, Pavel Škaloud, Eliška Záveská, Roswitha Schmickl
!!! The course is not opened for this year (2018)
For older presentations and tutorials see those from 2013 and 2016

DNA sequences I
Lesson 1 (5.10.2018)
Alignment and Sanger sequence editing, DNA saturation, basic single-gene tree construction
programs: BioEdit, HyPhy, SiteStripper, SplitsTree, PartitionFinder, RAxML, PAUP
presentation, tutorial


DNA sequences II
Lesson 2 (19.10.2018 - !!! will be exceptionally in KOL room, ground floor)
Species tree reconstruction, networks, incongruence tests
programs: *BEAST, SplitsTree, PhyloNet, Concaterpillar
presentation, tutorial


DNA sequences III - HybSeq
Lesson 3 (2.11.2018)
Multi-gene species tree reconstruction
programs: summary methods (ASTRAL, ASTRID), supertree (MRL)
presentation, tutorial


Microsatellites
Lesson 4 (23.12.2018)
population genetic parameters and detection of genetic structure in multilocus data, hybrid detection
programs: MSA, R (adegenet, pegas), Structure, FSTAT, NewHybrids, PAST
presentation, tutorial


SNP data
Lesson 5 (14.12.2018)
Structure and population genetic parameters in single nucleotide polymorphism (SNP) data, hierarchical structure in data (AMOVA), geographic covariates of genetic structure
programs: R (vcfR, adegenet, pegas, StAMPP)
presentation, tutorial


Combined analyses
Lesson 6 (4.1.2019)
Analysis of phenotypic data in phylogenetic context, species delimitation, submission of sequences to GenBank...
programs: Sequin, BEAST, R (ape, splits, phytools)
presentation, tutorial


Materials from a workshop on Population genetics of polyploids organized by Filip Kolář, Patrick Meirmans, Marc Stift & Martin Certner in Prague 1/2017 are here