Course – 3rd Edition
Quantitative Cladistics and Use of TNT
October 2nd-6th, 2017, Barcelona (Spain)
Evolution
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Course Overview
This course will cover the basics of parsimony analysis and character optimisation, tree-searches, diagnosing and summarising results efficiently, and measuring group supports.
This course will be informal, with extensive hands-on exercises which will help students get familiar with the main aspects of phylogenetic analysis using TNT. For each of the units in the course, there will be a lecture (one to two hours, depending on the topics), then switching to exercises illustrating the points just seen in the lecture. Switches between “lecture” and “hands-on” mode will be dynamic, depending on how students progress with the exercises.
This course will make extensive use of TNT. There will also be a demonstration and some practice with GB->TNT, a program to create TNT matrices from GenBank data (in turn, GB->TNT requires installation of an alignment program, ideally Mafft or Muscle and possibly BioEdit to inspect alignments).
REQUIREMENTS
Graduate or postgraduate degree in any Biosciences discipline (including palaeontologists no matter the degree), basic knowledge of statistics, cladistics and personal computers. All participants must bring their own personal laptop, Windows strongly recommended (the software works with Macintosh, though without a graphic interface).
Contact
LOCATION
DATE
January 13th-17th, 2020
LANGUAGE
English
COURSE LENGTH & ECTS
40 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 18 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. Pablo A. Goloboff
Fundación Miguel Lillo – CONICET
Argentina
Dr. Claudia A. Szumik
Fundación Miguel Lillo – CONICET
Argentina
Dr. Soledad De Esteban-Trivigno
Transmitting Science
Dr. Ana Rosa Gómez Cano
Transmitting Science
Contact: courses@transmittingscience.com
Program
Daily Program
Monday, October 2nd, 2017. Intro and Basics.
Parsimony and phylogenetic systematics. Character optimisation and mapping. Most parsimonious reconstructions and specific changes. Input/output in TNT. Dataset formats. Using GB->TNT to create matrices. Instruction files. Options for graphic output (SVG, metafiles). Creation of “batch” files. Editing trees. Handling tree files. Groups of trees, characters and taxa.
Tuesday, October 3rd, 2017. Tree calculation.
Tree searches. Exact solutions, Wagner trees, branch-swapping. Local and global optima. Use of multiple addition sequences. Improving search strategies. Factors which affect the efficiency of tree-searches. Constraints and “timeouts”.
Tuesday, October 3rd and Wednesday, October 4th, 2017. Ambiguity and consensus; summarizing results.
Zero-length branches and collapsing rules. Types of consensus and their use; improving consensus trees; supertrees. Pruned consensus. Comparison of tree-topologies; SPR distances.
Wednesday, October 4th, 2017. Character weighting.
Successive and implied weighting. Auto-weighted optimization. Refining character weighting with blocks; taking into account missing entries. User-defined weighting functions.
Thursday, October 5th, 2017. Group supports.
Concept of group support. Bremer supports; how to calculate them; search of suboptimal trees. Problems with Bremer supports; absolute and relative Bremer support. Partitioned Bremer support and individual Bremer supports. Measures based on resampling; effect of search strategies and collapsing rules. Problems with resampling methods.
Thursday, October 5th and Friday, October 6th, 2017. Tree search in large and difficult data sets.
Special search algorithms. Sectorial searches. Ratchet and drifting. Tree fusing. Combining different algorithms. Driven searches and stabilization of consensus.
Friday, October 6th, 2017. Scripting.
Automation of decisions to go beyond simple commands. Flow control. Decisions. Expressions, user variables, and internal variables. Design of simple scripts.
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.
Related Courses
Introduction to Macroevolutionary Analyses Using Phylogenies
May 29th - June 2nd, 2023 (ONLINE)
Transmitting Science started in 2012 to manage specialized courses and workshops we were already organizing within our own partnerships. Up to date, we have already run more than 120 advanced courses in different topics related to Life Sciences.
All the courses are self-financed with participant’s fees and we strive to keep the fees to the minimum necessary for running them.
Our courses cover a wide range of research methods and are aimed at postgraduate students, postdoctoral researchers and established academics from all over the world.
