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Phylogenetic data analysis using R (PHYL01)
31st October 2016 - 4th November 2016510£ - 620£
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.
Venue – Millport – Google Map – Directions
*Please note that Millport Field Station is very easy to reach using public transport.
Availability – 30 places
Duration – 5 days
Contact hours – Approx. 35 hours
ECT’s – Equal to 3 ECT’s
Language – English
We offer two packages
• COURSE ONLY – Includes lunch and refreshments.
• ALL INCLUSIVE – For an additional £210.00. Includes breakfast, lunch, dinner, refreshments, minibus to and from meeting point and accommodation. Accommodation is multiple occupancy (max 2 people) single sex en-suite rooms. Arrival Sunday 29th October and departure Friday 4th November December PM.
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To book ‘ALL INCLUSIVE’ first book ‘COURSE ONLY’ and then add accommodation and meals direct from the venue for £210.00 by clicking – HERE
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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 Millport field station at approximately 18:30 (Download directions PDF)
Monday 30th – 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 1st – 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 2nd – 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 3rd – 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 4rth – Classes from 09:00 to 16:00
Tree comparison, consensus methods.
Topological space and distances.