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Advanced Courses in Life Sciences

1st Edition

Introduction to Phylogenomics

October 7th-11th, 2019, Valencia (Spain)


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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


Campus of Gandía
Universidad Politécnica de Valencia

Street Paranimf, 1
46730 Grao de Gandia, Gandia
Valencia (Spain)


October 7th-11th, 2019




35 hours on-site.

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 20 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


Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science


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

All participants must bring their own personal laptop.


Monday, October 7th, 2019.

  • Morning: Nature of phylogenomic data (e.g., Rad-Seq, UCEs, exon capture, whole-genome resequencing); Stochastic and systematic error.
  • Afternoon: (Practical) Fundamentals of computing and bioinformatics.

Tuesday, October 8th, 2019.

  • Morning: Inferring individual gene trees with maximum likelihood (ML) and Bayesian methods; Bootstrapping.
  • Afternoon: (Practical) Model selection and gene-tree inference (e.g., IQTree, RevBayes) across thousands of genes.

Wednesday, October 9th, 2019.

  • Morning: Concatenated analysis; species tree inference; multi-species coalescent.
  • Afternoon: (Practical) Species tree inference (e.g., *BEAST, SVD Quartets, ASTRID/ASTRAL, SNAPP, SplitSup).

Thursday, October 10th, 2019.

  • Morning: Other sources of gene tree variation; tradeoffs between complexity and speed; Model adequacy.
  • Afternoon: (Practical) Applying these approaches in RevBayes and IQTree.

Friday, October 11th, 2019.

  • Morning: Interrogating, exploring, and visualizing the results of phylogenomic analysis.
  • Afternoon:(Practical) Application of these approaches with RevBayes, IQTree, TreeScaper, etc.


  • Course Fee
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  • Early bird (until June 30th, 2019):
  • 565 *

    (452 for Ambassador Institutions)

  • Regular (after June 30th, 2019):
  • 695 *

    (556 for Ambassador Institutions)

  • This includes course material, coffee breaks and lunches (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.
  • Course Fee + Accommodation Package
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  • Early bird (until June 30th, 2019):
  • 565 * + 320 = 885

    (772 for Ambassador Institutions)

  • Regular (after June 30th, 2019):
  • 695 * + 320 = 1,015

    (876 for Ambassador Institutions)

  • This includes course material, coffee breaks, transportation from and to Valencia city, accommodation from Sunday to Friday, breakfasts, lunches and dinners (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.

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

Discounts (see Funding below) are not cumulative and apply only on the fee.

We offer the possibility of paying in two instalments (contact the course coordinator).


Accommodation Package

If you take the Accommodation Package you will be hosted in the Cibeles Hotel, in single-sex shared dormitories (2 – 3 people) with bathroom en-suite.

A supplemental charge will be added if you prefer to stay in a single room.

Accommodation is included from Sunday (check-in) to Friday (check-out). Breakfast, lunch and dinner are also provided during the week, starting from the dinner of Sunday to lunch of Friday (included).

Hotel Cibeles is located at 3 blocks from the Venue and 3 blocks from the beach.


Hotel Cibeles

Hotel Cibeles


Course Schedule
  • Monday to Friday:
    • 9:30 to 13:30 Lessons.
    • 13:30 to 15:00 Lunch (included).
    • 15:00 to 18:00 Lessons.
Accommodation Package Schedule
  • Sunday:
    • 19:00 Meeting point in Estación del Norte (Valencia train station) to take the bus to Grao de Gandía.
    • 20:00 Registration in the Hotel.
    • 20:30 Dinner.
  • Monday to Thursday:
    • 8:00 to 9:00 Breakfast.
    • 20:30 Dinner.
  • Friday:
    • 8:00 to 9:00 Breakfast.
    • 20:30 Dinner.
    • 18:00 Meeting point in the Venue to take the bus to Valencia city.
    • 19:00 Arrival at Estación del Norte (Valencia train station).

    Valencia train station is connected with Valencia Airport by subway. There will be more information about how to get there soon. The schedule is approximate; it is possible that the content of one day may run into the next and a working day may be longer than advertised.



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

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

Unemployed scientists living in Spain, as well as PhD students based in Spain 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.

Discounts are not cumulative and apply only on the fee, not to Accommodation Package or other options.


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