This course will cover the basics of parsimony analysis and character optimisation, tree-searches, diagnosing and summarising results efficiently, and measuring group supports.
The 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.
The 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).
Dr. Pablo Goloboff
Dr. Claudia Szumik
Dr. Soledad De Esteban-Trivigno
(Transmitting Science, Spain).
Graduate or postgraduate degree in any Biosciences discipline (including palaeontologists no matter the degree), basic knowledge in 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).
|1st Day.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.
2nd Day. 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”.
2nd and 3rd Days. 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.
|3rd Day. Character weighting.
Successive and implied weighting. Auto-weighted optimization. Refining character weighting with blocks; taking into account missing entries. User-defined weighting functions.
4th Day. 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.
4th and 5th Days. 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.
5th Day. Scripting.
Automation of decisions to go beyond simple commands. Flow control. Decisions. Expressions, user variables, and internal variables. Design of simple scripts.
40 hours on-site.
18:00: Meeting point in Plaza Catalunya (Barcelona) to take the bus to Els Hostalets de Pierola. If you are planning to arrive later, you can find more information in How to arrive.
8:30 to 9:00: Breakfast
8:30 to 9:00: Breakfast.
Places are limited to 25 participants and will be occupied by strict registration order.
All Inclusive option:
Reduced registration fee until February 28, 2013: 625 € (415 € course fee + 210 € All Inclusive option). Full registration fee after February 28, 2013: 765 € (555 € course fee + 210 All Inclusive option).
Participation fees are all inclusive, and include transport from Barcelona city, course material, lodging, breakfasts, coffee breaks, lunches, dinners and welcome party.
Only Lunches Included option (no accommodation, no dinners):
This option only includes course material, coffee breaks and lunches. Please be aware that from Barcelona centre it takes one hour by car and one hour and a half by public transport to arrive to Els Hostalets de Pierola.
Reduced registration fee until February 28, 2013: 415 €. Full registration fee after February 28, 2013: 555 €.
Former participants will have a 5 % discount on the current course fee.
We offer the possibility of paying in two instalments (contact us at firstname.lastname@example.org).
Please complete and submit your Registration Form (see below); we will confirm your acceptance by e-mail.
|This course can be recognized, after evaluation, for 2 Credits by the Faculties of Science and Bioscience of the Universitat Autònoma de Barcelona - UAB.|
If you wish to cancel your participation in this course, cancellations up to 20 days before the course start date will incur a 30 % cancellation fee. For later cancellations, or non-attendance, the full course fee will be charged.
If Transmitting Science must cancel this course due to unforeseen circumstances beyond the control of Transmitting Science, you will either be entitled to a full refund of the course fee, or your fee can be credited toward a future course/workshop. Transmitting Science is not responsible for travel fees, or any expenses incurred by you as a result of such cancellation. Every effort will be made to avoid the cancellation of any planned course/workshop.
The course will take place in the town of Els Hostalets de Pierola, Barcelona (Spain).
- All Inclusive option:
To make it affordable, you will be hosted in four-bed dormitories (common bathrooms), although you will only share rooms with other classmates. The possibility exists that the dormitories will be mixed. Therefore, if this is an inconvenience for you, and you require staying in a dormitory with only women, or only men, please state it in the “Comments” field of the Registration Form (see below).
There are no Hotels in Els Hostalets de Pierola. However, if you do not want to share rooms with other participants, the council offers the possibility of renting a house (no kitchen available). If you want more information regarding this option, please contact us at email@example.com.
How to arrive to Els Hostalets de Pierola.
- Only Lunches Included option (no accommodation, no dinners):
In that case there are different options for accommodation, all of them in places other than Els Hostalets de Pierola. You may stay in: Barcelona city, Martorell or Igualada. Information about Hotels in Martorell here. Information about Hotels in Igualada here.
How to arrive to Els Hostalets de Pierola from Barcelona city, Martorell and Igualada.
Unfortunately there are no internal grants available for this course. For information on External Financial Support, please check the link.
For further information contact: firstname.lastname@example.org.