Dear all,
We are excited to announce our upcoming online course on Phylogenomics, focused on Phylogenetic Inference and Divergence-Time Estimation with Genomic Data Sets.
This course aims to provide researchers with the necessary tools and techniques to harness the power of genomic data for understanding evolutionary relationships and divergence times.
- Dates: 4-8 December 2023
- Format: Online to facilitate international participation
- Course website: : https://www.physalia-courses.org/courses-workshops/phylogenomics/
This course will equip participants with the theoretical knowledge and practical skills needed to confidently infer time-calibrated phylogenies from multi-locus genome data sets, while accounting for these challenges.
This course is tailored for researchers, PhD candidates, and postdocs aiming to infer phylogenetic relationships and divergence times from multilocus data, regardless of prior experience. Whether you're new to the field or seeking to enhance your skills, this course is designed to cater to a diverse range of learners.
Monday – Classes from 2 to 8 pm Berlin time
Lecture: Basic phylogenetics concepts
- Overview of phylogenetic inference methods
- Challenges
- Substitution models
- Maximum likelihood inference
Lab: Sequence alignment/filtering
- Alignment with MAFFT and alignment filtering
- Model selection
- Maximum likelihood phylogenetic inference with RAxML and IQTree
- Likelihood calculation - optional
Tuesday – Classes from 2 to 8 pm Berlin time
Lecture: Bayesian inference - MCMC
Lab: Phylogenetic inference methods
Introduction to MCMC in R
- Bayesian phylogenetic inference - MrBayes
Wednesday – Classes from 2 to 8 pm Berlin time
Lecture: The Multi- Species Coalescent
- Incomplete lineage sorting
- Approximate vs. Likelihood based methods
- Concatenation versus the multi-species coalescent - Case studies
Lab: Gene-tree / Species-tree Approaches
- Maximum-likelihood species-tree inference with ASTRAL
- Bayesian species-tree inference with BPP
Thursday – Classes from 2 to 8 pm Berlin time
Lecture 1: The Multi Species Coalescence with Introgression -Prof. Ziheng Yang (University College London)
Lab 1: Parameter estimation under the MSCi model
Lecture 2: Parallel Computing with phylogenomic software- possibilities and challenges
Lab 2: Parallelization with RAxML
Parallelization with BPP
Friday – Classes from 2 to 8 pm Berlin time
Lecture: Divergence times estimation
Lab: Divergence times estimation using MCMCTree and Beast
For the full list of our courses and Workshops, please have a look at: https://www.physalia-courses.org/courses-workshops
