Course – 1st Edition
Introduction to Phylogenetic Inference and its Applications
June 26th-30th, 2017, Barcelona (Spain)
Evolution
Python Machine Learning in Biology
November 16th-December 14th, 2023 (ONLINE)
REGISTRATION IS CLOSED
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Course Overview
The aim of this course is to provide training in conceptual and practical aspects of biological systematics. Emphasis will be on the use of molecular data for phylogenetic inference. We will present and discuss the main methods of phylogenetic inference (parsimony, maximum likelihood and Bayesian inference), evolutionary models, data combinability, the estimation of divergence times and the use of quantitative approaches to species delimitation. We will also discuss several examples about the use of phylogenetic trees to address fundamental biological questions. In hands on computer sessions, we will introduce the most widely used computer programs for building alignments, selecting evolutionary models, inferring trees under alternative assumptions, estimating divergence times and delimiting species. Finally, students will present and discuss the results obtained during the course using their own data or, alternatively, with example cases provided by the instructors.
The course is aimed at advanced undergrads, PhD students, post-docs and faculty interested in the use of phylogenies for addressing evolutionary and ecological questions but with limited background / experience in systematics and phylogenetic inference.
REQUIREMENTS
Basic knowledge of statistics. All participants must bring their own personal laptop.
Contact
LOCATION
DATE
January 13th-17th, 2020
LANGUAGE
English
COURSE LENGTH & ECTS
32 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
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.
Dr. Miquel Arnedo
Universitat de Barcelona
Spain
Dr. Salvador Carranza
Institute of Evolutionary Biology (CSIC-UPF)
Spain
Dr. Soledad De Esteban-Trivigno
Transmitting Science
Dr. Ana Rosa Gómez Cano
Transmitting Science
Contact: courses@transmittingscience.com
Program
Daily Program
Monday, June 26th, 2017.
- Introduction to biological and molecular systematics, the basis and principles of phylogenetic inference.
- Gene tree vs. species tree. Homology and alignments.
- Hands on: Data format, Clustal, MAFFT, Gblocks, SeqState.
Tuesday, June 27th, 2017.
- Morphological data: coding, ordering and polarity.
- Gap treatment. Implicit weighting. Support and sensibility.
- Understanding phylogenies.
- Hands on: Mesquite, TNT.
Wednesday, June 28th, 2017.
- Evolutionary models and genetic distances.
- Algorithmic approaches to tree building, Maximum Likelihood and Bayesian Inference. Toplogy test.
- Hand on: PartitionFinder, jModeltest, MEGA; MrBayes; RaxML, CONSEL.
Thursday, June 29th, 2017.
- Morphology and Phylogeny, integrating morphological and molecular data.
- Dating.
- Hands on: BEAST, *BEAST.
Friday, June 30th, 2017.
- DNA and Integrative taxonomy: DNA barcoding, species trees and quantitative species delimitation.
- Hands on: SPLITS (GMYC), BPP.
Fees
- Course Fee
- Early bird (until October 31st, 2019):
- 476 € *
(380.80 € for Ambassador Institutions) - Regular (after October 31st, 2019):
- 595 € *
(476 € 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
- Early bird (until October 31st, 2019):
- 826 € * (660.80 € for Ambassador Institutions)
- Regular (after October 31st, 2019):
- 945 € * (756 € for Ambassador Institutions)
- This includes course material, coffee breaks, transportation from and to Barcelona 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. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.com
Schedule
Course Schedule
Participants will make their own way
- Monday to Friday:
- 9:00 to 13:30 Lessons.
- 13:30 to 14:30 Lunch (included).
- 14:30 to 18:00 Lessons.
The class 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.
Course + Accommodation Package Schedule
- Sunday:
- 19:00 Meeting point in Plaza Catalunya (Barcelona) to take the bus to Capellades. If you are planning to arrive later, you can find more information on how to get there.
- 20:00 Registration in the Hostel.
- 20:30 Dinner.
- Tuesday to Thursday:
- 08:00 to 09:00 Breakfast
- 9:00 to 13:30 Lessons
- 13:30 to 14:30 Lunch (included)
- 14:30 to 18:00 Lessons
- 20:00 Dinner
- Friday:
- 8:00 to 9:00 Breakfast.
- 9:30 to 13:30 Lessons
- 13:30 to 14:30 Lunch (included)
- 14:30 to 18:00 Lessons
- 18:00 Meeting in Hotel to take the bus to Barcelona city.
- 19:30 Arrival at Plaça Catalunya (Barcelona)
The class 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.
Accommodation
If you choose the Accommodation Package you will be hosted at Rural House Can Carol, in shared en-suite rooms, although you will only share rooms with other course participants (male or female only).
If you prefer to stay in a single en-suite room, you can do so with a supplementary charge.
More information
The Accommodation Package includes transportation from the centre of Barcelona city to the venue and back, at the start and end of the course, respectively. The trip takes around 1 hour each way.
If the number of participants exceeds the available rooms at Can Carol, some of them could be accommodated in the Hotel Tall del Conill, by registration order. The hotel is at 10 minutes walking, although transport will be provided in the morning and after dinner. Lunches and dinners will be with the whole group.
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).
Other accommodation options
If you do not want the Accommodation Package, accommodation is available in places other than Can Carol: Where to stay near the Venue.
Funding
Discounts are not cumulative and apply only on the Course Fee. We offer the possibility of paying in two instalments (contact courses@transmittingscience.com).
5 % Discount
Former participants will have a 5 % discount on the Course Fee.
20 % Discount
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).
40 % Discount
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.
