ForBio and Transmitting Science course: 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.
Online live sessions from Monday 19th to Friday 23rd ((GMT+2, Madrid time zone)
- 08:00-10:30 – Morning live session
- 10:30-11:30 – Break
- 11:30-14:00 – Afternoon live session
Phylogenetic data with R.
- 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.
- Theory of sequence alignment. Comparing alignments. Graphical analyses of alignments.
Phylogenetic reconstruction with distance-based methods.
- 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.
Phylogenetic reconstruction with maximum likelihood methods.
- Theory of maximum likelihood and application to phylogeny reconstruction. Substitution models. Tree space and topology estimation. Introduction to the package phangorn.
Tree space and tree comparison.
- Tree comparison, consensus methods, topological space and distances, bootstrap and Bayesian methods.
- 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.
Course duration: 30 hours, 25 hours live online and 5 hours of exercises between the live sessions.
Coordinator: Hugo de Boer (firstname.lastname@example.org) – ForBio.
Credits: A 1 ECTS course certificate will be given to students that pass the course.
Level: Graduate or postgraduate degree in any Biosciences discipline. Knowledge of multivariate statistics, phylogenetics and molecular evolution. User level of R. All participants must have a personal computer (Windows, Macintosh), with webcam if possible, and a good internet connection.
Participants: Maximum 16.
Application deadline: April 30th, 2021 (For ForBio members).
Fee: ForBio has a limited number of course waivers for this course for ForBio members (MSc and PhD students, and postdocs). ForBio associates can get a 20% discount on the course fee.
Click here for more information about the course.
For those interested in registering in this course, please do so through the Transmitting Science website.