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Online Course – 3rd Edition

Introduction to Phylogenomics

November 4th, 6th, 8th, 11th, 13th, 15th, and 18th, 2024

Registration

Contact: courses@transmittingscience.com

Introduction to Phylogenomics

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Course Overview

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

Places are limited to 18 participants.

Programme

  • 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.

Assumed Background

Graduate or postgraduate degree in any Biosciences discipline. Some previous experience running phylogenetic analyses will be helpful.

Sotfware

Example software: RevBayes, IQTree, SVDQuartets, ASTRAL, TreeScaper

Dates & Schedule

Online live sessions on November 4th, 6th, 8th, 11th, 13th, 15th, and 18th, 2024.

From 18:00 to 21:00 (Madrid time zone).

Total course hours: 28 (21 hours of online live lessons, plus 7 hours of students working by their own).

This course is equivalent to 1 ECTS (European Credit Transfer System). The recognition of ECTS by other institutions depends on each university or school.

Format

In the live sessions we will combine online lectures with hands-on computational exercises.

Live sessions will be recorded. However, attendance to the live sessions is required to obtain the course certificate.

Instructors

Jeremy M Brown instructor for Transmitting Science

Dr. Jeremy M Brown 
Louisiana State University
United States of America

Robert Thomson instructor for Transmitting Science

Dr. Robert Thomson
University of Hawaii
United States of America

Registration Fees

  • Course Fee
  • Early bird (until September 30th, 2024):
  • 510 €
    (408 € for Ambassador Institutions)
  • Regular (after September 30th, 2024):
  • 580 €
    (464 € for Ambassador Institutions)
  • Prices include VAT.
    After registration you will receive confirmation of your acceptance on the course.
    Payment is not required during registration. Check discounts here.
  • How do I get the Ambassador Institution discount?
  • Registration

Organiser

Logo Transmitting Science

Collaborators

Logo COBCYL
Logo COBCV
Logo COBEUSKADI
Logo COBGA