News:Course on Phylogenomics
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26 days ago
carlopecoraro2 ★ 2.3k

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.

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:

Phylogenetic-Inference Divergence-Time-Estimation Genomics Phylogenomics • 132 views

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