• Advanced Courses in Life Sciences

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Online Course – 2nd Edition

Introduction to Phylogenomics

October 1st-9th, 2020




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Introduction to PhylogenomicsCourse 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


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.




This course will be delivered online.

Please check the schedule for the live online part, and be aware that it is GMT+1.


October 1st-9th, 2020




35 hours online.

This course is equivalent to 2 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.


Places are limited to 16 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end of it.

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


  • 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 €.

You can check the list of Ambassador Institutions. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.com


The live classes will run on week days. Thursday 1st to Friday 2nd and Monday 5th to Friday 9th.

  • 18:00 to 21:00 online live lessons (GMT+1).

The rest of the time will be taught with recorded classes and assignments, to be done between the live sessions.


Discounts are not cumulative and apply only on the Course Fee. We offer the possibility of paying in two instalments (contact courses@transmittingscience.com).

Former participants will have a 5 % discount on the Course Fee.

20 % discount on the Course Fee is offered for members of some organizations (Ambassador Institutions). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Unemployed scientists living in the country were the course will be held, as well as PhD students based in that country without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.