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Advanced Courses in Life Sciences

4th Edition

Phylogenetic Analysis Using R

March 6th-10th, 2017, Barcelona (Spain)

Phylogenetic Analysis Using R

This course is for biologists dealing with the analysis of multiple molecular sequences at several levels: Populations, species, clades, communities. These biologists address questions relative to the evolutionary relationships among these sequences, as well as the evolutionary forces structuring biodiversity at different scales.

The objectives of the course are: (i) to know how to choose a strategy of molecular data analysis at the inter‐ or intraspecific levels, (ii) to be able to initiate a phylogenetic analysis starting from the files of molecular sequences until the interpretation of the results and the graphics.

The software used for this course will be centered on the R language for statistics. This will include the use of specialized packages particularly ape, phangorn, and adegenet.

LOCATION

Centre de Restauració i Interpretació Paleontològica

C/ Mestre J. Lladós, nº 1
08781 Els Hostalets de Pierola, Barcelona.

Spain – CRIP

LANGUAGE

English

COURSE LENGHT & ECTS

35 hours on-site.

This course is equivalent to 3.5 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School and ForBio.

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

PLACES

Places are limited to 25 participants and will be occupied by strict registration order.

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

Instructors

Emmanuel Paradis instructor for Transmitting Science

Dr. Emmanuel Paradis
Institut de Recherche pour le Développement
France

Klaus Schliep instructor for Transmitting Science

Dr. Klaus Schliep
University of Massachusetts Boston
United States of America

Coordinators

Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science
Spain

Judit Marigó coordinator at Transmitting Science

Dr. Judit Marigó
Muséum national d’Histoire naturelle / Institut Català de Paleontologia Miquel Crusafont
France / Spain

Requirements

Graduate or postgraduate degree in any Biosciences discipline. Knowledge of multivariate statistics, phylogenetics and molecular evolution. User level of R. All participants must bring their own personal laptop (Windows, Macintosh, Linux).

Program

Monday, March 6th, 2017. Phylogenetic data with R.

  • Morning: Basics on phylogenetic data (sequences, alignments, trees, networks, “splits”) and other data in R. Reading / writing data from files or from internet. Matching data. Manipulating labels. Subsetting data.
  • Afternoon: Applications.


Tuesday, March 7th, 2017. Managing sequences.

  • Morning: Theory of sequence alignment. Comparing alignments. Graphical analyses of alignments.
  • Afternoon: Applications.


Wednesday, March 8th, 2017. Phylogenetic reconstruction with distance-based methods.

  • Morning: Theory and methods of phylogeny reconstruction. Comparison of methods. The variance of distances. Distance-based methods: General principles and the main methods (NJ, BIONJ, FastME, MVR). Methods for incomplete distances matrices (NJ*, BIONJ*, MVR*). Methods for combining several matrices (SDM). Parsimony methods.
  • Afternoon: Applications.

Thursday, March 9th, 2017. Phylogenetic reconstruction with maximum likelihood methods.

  • Morning: Theory of maximum likelihood and application to phylogeny reconstruction. Substitution models. Tree space and topology estimation. Introduction to the package phangorn.
  • Afternoon: Applications.



Friday, March 10th, 2017. Tree space and tree comparison.

  • Morning: Tree comparison, consensus methods, topological space and distances, bootstrap and Bayesian methods.
  • Afternoon: Applications.

Books

  • Felsenstein J (2004) Inferring phylogenies, Sunderland: Sinauer Associates.
  • Lemey P, Salemi M and Vandamme A-M (2009) The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing (Second Edition), Cambridge: Cambridge University Press.
  • Paradis E (2012) Analysis of Phylogenetics and Evolution with R (Second Edition), New York: Springer.

Testimonials

You will find below some testimonials from former participants to previous editions of this course:

Dr. Susanna López-Legentil

“This course is a ‘must’ for any researcher working on phylogenetics. The instructors do an outstanding job of explaining the potential of the available packages and what you can do and cannot do (mostly ‘can’, as with R it is all a matter of writing new functions / commands to get your answers!). I enjoyed this course thoroughly and I will certainly apply all I have learned to my current research!” (1st Edition)

Dr. Susanna López-LegentilUniversity of Barcelona, Spain

Fees

  • Course Fee
  • Early bird (until November 30th, 2016)
  • 565
  • Regular (after November 30th, 2016)
  • 790
  • This includes course material, coffee breaks and lunches.
  • Accommodation Package
  • Early bird (until November 30th, 2016)
  • 360
  • Regular (after November 30th, 2016)
  • 360
  • This includes local transportation, lodging, breakfasts, dinners and social (tourist) activities.
  • Course Fee + Accommodation Package
  • Early bird (until November 30th, 2016)
  • 925
  • Regular (after November 30th, 2016)
  • 1,150
  • This includes course material, coffee breaks and lunches.

We offer the possibility of paying in two instalments (contact the course coordinators). Discounts (see Funding below) are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Accommodation

If you take the Accommodation Package you will be hosted in the Youth Hostel Can Roviralta, in shared 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 indicate so in the “Comments” field of the Registration form (see below).

A supplemental charge will be added if you prefer to stay in a single room with private bathroom. The number of rooms is limited and if you prefer to have a single room, let us know it as soon as possible. If you want more information on this please contact the course coordinators.

Please be aware that from the centre of Barcelona city it takes about one hour by car and one hour and a half by public transport to arrive to Els Hostalets de Pierola. Course participants will find that staying in Els Hostalets de Pierola is more convenient.

If you do not want the Accommodation Package, accommodation is available in places other than Els Hostalets de Pierola. You may stay in Barcelona city, Martorell or Igualada. You will find information about Hotels in Martorell here, and information about Hotels in Igualada here.

How to get to Els Hostalets de Pierola from Barcelona city, Martorell and Igualada.

Youth Hostel Can Roviralta (Els Hostalets de Pierola, Barcelona, Spain)

Funding

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

Unfortunately there are no scholarships available for this course. However 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).

Spanish unemployed scientists, as well as Spanish PhD students 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 coordinators. 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.

Schedule

Course ScheduleCourse + Accommodation Package Schedule
Sunday, March 5th, 201719:00 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 get there.
20:00 Registration in the Youth Hostel.
20:30 Dinner.
Monday, March 6th through Friday, March 10th, 20179:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 18:00 Lessons.

There will be two coffee breaks each day, halfway through each lesson session.

8:30 to 9:00 Breakfast.
9:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 18:00 Lessons.
20:30 Dinner.

There will be two coffee breaks each day, halfway through each lesson session.

Saturday, March 11th, 20178:30 to 9:00 Breakfast.
9:15 Meeting point in the Youth Hostel to take the bus to visit a wine cellar.
10:00 Arrival at the wine cellar.
11:30 Bus to Barcelona city.
13:00 Arrival at Plaza Catalunya (Barcelona).

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.

Organizers

Transmitting Science Logo
Research School in Biosystematics (ForBio) Logo
Centre de Restauració i Interpretació Paleontològica (CRIP) Logo
Institut Català de Paleontologia Miquel Crusafont (ICP) Logo

Collaborators

Colegio Oficial de Biólogos de Castilla y León Logo
Colegio Oficial de Biólogos de Euskadi Logo
Colexio Oficial de Biólogos de Galicia Logo
Col·legi Oficial de Biòlegs de la Comunitat Valenciana Logo
Distributed European School of Taxonomy (DEST) Logo
European Association of Vertebrate Palaeontologists (EAVP) Logo
Sociedade Brasileira de Paleontologia (SBP) Logo

Registration

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