This workshop will introduce participants to the theory and tools for phylogenetic inference in the era of genome sequencing. Course material will focus on statistical methods for phylogeny estimation, software implementing these methods, applications of these methods to large molecular datasets, and discuss trade-offs and tools for improving the accuracy of phylogenomic analyses. In hands-on practical sessions, participants will gain experience working with bioinformatic and statistical tools for analyzing large datasets.
The course is intended to facilitate ongoing or planned phylogenomics projects by students, so they are encouraged to notify instructors in advance about the topics of greatest relevance to their own work.
Example software: RevBayes, IQTree, SVDQuartets, ASTRAL, TreeScaper
Graduate or postgraduate degree in any Biosciences discipline. Some previous experience running phylogenetic analyses will be helpful.
All participants must have a personal laptop and a good internet connection.
- Nature of phylogenomic data (e.g., Rad-Seq, UCEs, exon capture, whole-genome resequencing); Stochastic and systematic error.
- Fundamentals of computing and bioinformatics.
- Inferring individual gene trees with maximum likelihood (ML) and Bayesian methods; Bootstrapping.
- Model selection and gene-tree inference (e.g., IQTree, RevBayes) across thousands of genes.
- Concatenated analysis; species tree inference; multi-species coalescent.
- Species tree inference (e.g., *BEAST, SVD Quartets, ASTRID/ASTRAL, SNAPP, SplitSup).
- Other sources of gene tree variation; tradeoffs between complexity and speed; Model adequacy.
- Applying these approaches in RevBayes and IQTree.
- Interrogating, exploring, and visualizing the results of phylogenomic analysis.
- Application of these approaches with RevBayes, IQTree, TreeScaper, etc.
- Course Fee
- Early bird (until August 15th, 2020):
- 548 € *
(438.4 € for Ambassador Institutions)
- Regular (after August 15th, 2020):
- 675 € *
(540 € for Ambassador Institutions)
- This includes course material (VAT included).
* Participants from companies/industry will have an extra charge of 100 €.