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Phylogenetic data analysis using R (PHYL02)
29 January 2018 - 2 February 2018£260.00 - £460.00
The main objectives of the course are to teach the theoretical bases of phylogenetic analysis, and to give the ability to initiate a phylogenetic analysis starting from the files of molecular sequences until the interpretation of the results and the graphics. The introduction will cover a brief historical background and an overview of the different methods of phylogenetic inference. Different kinds of data will be considered, but with a special emphasis on DNA sequences. The software used will be based on R and several specialized packages (particularly ape and phangorn). Other software will be used (e.g., MUSCLE or Clustal) called from R. Overall, the course will cover almost all aspects of phylogenetic inference from reading/downloading the data to plotting the results.
PhD and postgraduate students, researchers and engineers in evolutionary biology, systematics, population genetics, ecology, conservation.
We offer COURSE ONLY and ACCOMMODATION PACKAGES;
• COURSE ONLY – Includes lunch and refreshments.
• ACCOMMODATION PACKAGE (to be purchased in addition to the course only option) – Includes breakfast, lunch, dinner, refreshments, minibus to and from meeting point and accommodation. Accommodation is multiple occupancy (max 3 people) single sex en-suite rooms. Arrival Sunday 28th January and departure Friday 2nd February PM.
To book ‘COURSE ONLY’ with the option to add the additional ‘ACCOMMODATION PACKAGE’ please scroll to the bottom of this page.
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Cancellation policy: Cancellations are accepted up to 28 days before the course start date subject to a 25% cancellation fee. Cancellations later than this may be considered, contact firstname.lastname@example.org Failure to attend will result in the full cost of the course being charged. In the unfortunate event that PR~statistics must cancel this course due to unforeseen circumstances a full refund for the course will be credited. However PR~statistics cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.
The course will mix lectures and practicals. The participants are encourage to bring their own data to apply the methods and tools. Data sets could be provided or downloaded from Internet for those who do not (or cannot) bring their own data.
Assumed quantitative knowledge
A basic understanding of statistical inference, biological evolution, and genetics (DNA, nucleotides, chromosomes etc).
Assumed computer background
Familiarity with R. Ability to import/export data, manipulate files, repositories, edit a text file.
Equipment and software requirements
A laptop/personal computer with a working version or R and RStudio installed. R and RStudio are supported by both PC and MAC and can be downloaded for free by following these links.
It is essential that you come with all necessary software and packages already installed (you will be sent a list of packages prior to the course) internet access may not always be available.
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Meet at the Tullie Inn, Balloch at approximately 18:30 before being taken by minibus to SCENE (Download directions PDF)
Monday 29th – Classes from 09:00 to 17:00
Refresher on R: data structures, data manipulation with the indexing system, scripts, using
the help system.
Introduction to phylogenetic inference.
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.
Main package: ape.
Tuesday 30th – Classes from 09:00 to 17:00
Plotting and annotating trees.
Theory of sequence alignment. Comparing alignments. Graphical analyses of alignments.
Main packages: ape (with MUSCLE and Clustal).
Wednesday 31st – Classes from 09:00 to 17:00
Theory and methods of phylogeny reconstruction.
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).
Main packages: ape, phangorn.
Thursday 1st – Classes from 09:00 to 17:00
Theory of maximum likelihood estimation.
Application to phylogeny reconstruction.
Tree space and topology estimation.
Main packages: ape, phangorn.
Friday 2nd – Classes from 09:00 to 16:00
Tree comparison, consensus methods.
Topological space and distances.
The instructors were excellent and clearly were the reasons for my previous comments. They both combined a deep understanding of statistics and ecology at the same level.Any questions or queries I’ve had, were thus first answered with an ecological point of view and then translated into statistical consideration thereby making much more sense on both side.In addition the course was very well organised, the course director and the two instructors were very friendly as well as professional. On the top of learning many useful things, I’ve also had a very good time during the week there.” Clement Garcia,
Spatial ecologist, Centre For Environment, Fisheries & Aquaculture Science (CEFAS), England
(Attended ADVR course)