Advanced methods in DNA sequence and mulilocus data analyses - MB120P143

Lecturers: Filip Kolář, Eliška Záveská, Pavel Škaloud, Tomáš Fér
Time: Fridays 8:30 - 13:00, Place: Benátská 2, Seminarium (BB), 2nd floor
For previous presentations and tutorials (2013, in Czech) see here

DNA sequences I
Lesson 1 (21.10.2016)
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 (4.11.2016)
Species tree reconstruction, networks, incongruence tests
programs: *BEAST, SplitsTree, PhyloNet, Concaterpillar
presentation, tutorial


DNA sequences III - HybSeq
Lesson 3 (25.11.2016)
Multi-gene species tree reconstruction
programs: summary methods (ASTRAL, ASTRID), supertree (MRL)
presentation, tutorial


Microsatellites
Lesson 4 (9.12.2016)
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 (6.1.2017)
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 (13.1.2017)
Analysis of phenotypic data in phylogenetic context, species delimitation, submission of sequences to GenBank...
programs: Sequin, BEAST, R (ape, splits, phytools)
presentation, tutorial