[R-sig-genetics] PhylogeneticDataAnalysisInR. 28Jan-2Feb.Paradis.FINALCALL
Oliver Hooker
oliverhooker at prstatistics.com
Wed Nov 15 19:22:47 CET 2017
"Phylogenetic data analysis using R"
FINAL CALL - LAST FEW PLACES
Delivered by Dr. Emmanuel Paradis
www.prstatistics.com/course/introduction-to-phylogenetic-analysis-with-r-phyg-phyl02/
This course will run from 28th January - 2nd February 2018 at SCENE
field station, Loch Lomond, Glasgow.
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. This course is intended for PhD and
postgraduate students, researchers and engineers in evolutionary
biology, systematics, population genetics, ecology, conservation.
Course content is as follows
Day 1
• 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.
Day 2
• Plotting and annotating trees.
• Theory of sequence alignment. Comparing alignments. Graphical
analyses of alignments.
• Main packages: ape (with MUSCLE and Clustal).
Day 3
• Theory and methods of phylogeny reconstruction.
• Parsimony methods.
• Evolutionary 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).
• Main packages: ape, phangorn.
Day 4
• Theory of maximum likelihood estimation.
• Application to phylogeny reconstruction.
• Substitution models.
• Tree space and topology estimation.
• Main packages: ape, phangorn.
Day 5
• Tree comparison, consensus methods.
• Topological space and distances.
• Bootstrap.
• Bayesian methods.
Please email any inquiries to oliverhooker at prstatistics.com or visit our
website www.prstatistics.com
Please feel free to distribute this material anywhere you feel is
suitable
PRstatistics upcoming courses - email for details
oliverhooker at prstatistics.com for details
1. November 20th - 25th 2017
APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS #ABME
SCENE, Scotland, Dr. Matt Denwood
http://www.prstatistics.com/course/applied-bayesian-modelling-ecologists-epidemiologists-abme03/
2. November 27th – December 1st 2017
INTRODUCTION TO PYTHON FOR BIOLOGISTS #IPYB
Margam Discovery Centre, Wales, Dr. Martin Jones
http://www.prinformatics.com/course/introduction-to-python-for-biologists-ipyb04/
-----------------------------------------------------------------------------------------------------------------
3. December 4th - 8th 2017
ADVANCING IN STATISTICAL MODELLING USING R #ADVR
Margam Discovery Centre, Wales, Dr. Luc Bussiere, Dr. Tom Houslay, Dr.
Ane Timenes Laugen,
http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr07/
-----------------------------------------------------------------------------------------------------------------
4. January 29th – February 2nd 2018
INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING #IBHM
SCENE, Scotland, Dr. Andrew Parnell
http://www.prstatistics.com/course/introduction-to-bayesian-hierarchical-modelling-using-r-ibhm02/
5. January 29th – February 2nd 2018
PHYLOGENETIC DATA ANALYSIS USING R #PHYL
SCENE, Scotland, Dr. Emmanuel Paradis
https://www.prstatistics.com/course/introduction-to-phylogenetic-analysis-with-r-phyg-phyl02/
-----------------------------------------------------------------------------------------------------------------
6. February 19th – 23rd 2018
MOVEMENT ECOLOGY #MOVE
Margam Discovery Centre, Wales, Dr Luca Borger, Dr Ronny Wilson, Dr
Jonathan Potts
https://www.prstatistics.com/course/movement-ecology-move01/
7. February 19th – 23rd 2018
GEOMETRIC MORPHOMETRICS USING R #GMMR
Margam Discovery Centre, Wales, Prof. Dean Adams, Prof. Michael Collyer,
Dr. Antigoni Kaliontzopoulou
http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr01/
-----------------------------------------------------------------------------------------------------------------
8. March 5th - 9th 2018
SPATIAL PRIORITIZATION USING MARXAN #MRXN
Margam Discovery Centre, Wales, Jennifer McGowan
https://www.prstatistics.com/course/introduction-to-marxan-mrxn01/
9. March 12th - 16th 2018
ECOLOGICAL NICHE MODELLING USING R #ENMR
Glasgow, Scotland, Dr. Neftali Sillero
http://www.prstatistics.com/course/ecological-niche-modelling-using-r-enmr02/
10. March 19th – 23rd 2018
BEHAVIOURAL DATA ANALYSIS USING MAXIMUM LIKLIHOOD IN R #BDML
Glasgow, Scotland, Dr William Hoppitt
http://www.psstatistics.com/course/behavioural-data-analysis-using-maximum-likelihood-bdml01/
-----------------------------------------------------------------------------------------------------------------
11. April 9th – 13th 2018
NETWORK ANAYLSIS FOR ECOLOGISTS USING R #NTWA
Glasgow, Scotland, Dr. Marco Scotti
https://www.prstatistics.com/course/network-analysis-ecologists-ntwa02/
12. April 16th – 20th 2018
INTRODUCTION TO STATISTICAL MODELLING FOR PSYCHOLOGISTS USING R #IPSY
Glasgow, Scotland, Dr. Dale Barr, Dr Luc Bussierre
http://www.psstatistics.com/course/introduction-to-statistics-using-r-for-psychologists-ipsy01/
13. April 23rd – 27th 2018
MULTIVARIATE ANALYSIS OF ECOLOGICAL COMMUNITIES USING THE VEGAN PACKAGE
#VGNR
Glasgow, Scotland, Dr. Peter Solymos, Dr. Guillaume Blanchet
https://www.prstatistics.com/course/multivariate-analysis-of-ecological-communities-in-r-with-the-vegan-package-vgnr01/
14. April 30th – 4th May 2018
QUANTITATIVE GEOGRAPHIC ECOLOGY: MODELING GENOMES, NICHES, AND
COMMUNITIES #QGER
Glasgow, Scotland, Dr. Dan Warren, Dr. Matt Fitzpatrick
https://www.prstatistics.com/course/quantitative-geographic-ecology-using-r-modelling-genomes-niches-and-communities-qger01/
-----------------------------------------------------------------------------------------------------------------
15. May 7th – 11th 2018 ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL
ECOLOGICAL DATA USING R #MVSP
CANADA (QUEBEC), Prof. Pierre Legendre, Dr. Guillaume Blanchet
https://www.prstatistics.com/course/advances-in-spatial-analysis-of-multivariate-ecological-data-theory-and-practice-mvsp03/
16. May 14th - 18th 2018
INTRODUCTION TO MIXED (HIERARCHICAL) MODELS FOR BIOLOGISTS #IMBR
CANADA (QUEBEC), Prof Subhash Lele
https://www.prstatistics.com/course/introduction-to-mixed-hierarchical-models-for-biologists-using-r-imbr01/
17. May 21st - 25th 2018
INTRODUCTION TO PYTHON FOR BIOLOGISTS #IPYB
SCENE, Scotland, Dr. Martin Jones
http://www.prinformatics.com/course/introduction-to-python-for-biologists-ipyb05/
18. May 21st - 25th 2018
INTRODUCTION TO REMOTE SENISNG AND GIS FOR ECOLOGICAL APPLICATIONS
Glasgow, Scotland, Prof. Duccio Rocchini, Dr. Luca Delucchi
https://www.prinformatics.com/course/introduction-to-remote-sensing-and-gis-for-ecological-applications-irms01/
19. May 28th – 31st 2018
STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR #SIMM
CANADA (QUEBEC) Dr. Andrew Parnell, Dr. Andrew Jackson
https://www.prstatistics.com/course/stable-isotope-mixing-models-using-r-simm04/
20. May 28th – June 1st 2018
ADVANCED PYTHON FOR BIOLOGISTS #APYB
SCENE, Scotland, Dr. Martin Jones
https://www.prinformatics.com/course/advanced-python-biologists-apyb02/
-----------------------------------------------------------------------------------------------------------------
21. June 12th -0 15th 2018
SPECIES DISTRIBUTION MODELLING #DBMR
Myuna Bay sport and recreation, Australia, TBC
COMING SOON www.PRstatistics.com
22. November 6th – 10th 2017
LANDSCAPE GENETIC DATA ANALYSIS USING R #LNDG
Myuna Bay sport and recreation, Australia, TBC
COMING SOON www.PRstatistics.com
23. June 18th – 22nd 2018
STRUCTURAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY BIOLOGISTS
USING R #SEMR
Myuna Bay sport and recreation, Australia, TBC
COMING SOON www.PRstatistics.com
-----------------------------------------------------------------------------------------------------------------
24. July 2nd - 5th 2018
SOCIAL NETWORK ANALYSIS FOR BEHAVIOURAL SCIENTISTS USING R #SNAR
Glasgow, Scotland, Prof James Curley
http://www.psstatistics.com/course/social-network-analysis-for-behavioral-scientists-snar01/
25. July 8th – 12th 2018
MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R #MBMV
Glasgow, Scotland, Prof David Warton
https://www.prstatistics.com/course/model-base-multivariate-analysis-of-abundance-data-using-r-mbmv02/
26. July 16th – 20th 2018
PRECISION MEDICINE BIOINFORMATICS: FROM RAW GENOME AND TRANSCRIPTOME
DATA TO CLINICAL INTERPRETATION #PMBI
Glasgow, Scotland, Dr Malachi Griffith, Dr. Obi Griffith
https://www.prinformatics.com/course/precision-medicine-bioinformatics-from-raw-genome-and-transcriptome-data-to-clinical-interpretation-pmbi01/
27. July 23rd – 27th 2018
EUKARYOTIC METABARCODING
Glasgow, Scotland, Dr. Owen Wangensteen
http://www.prinformatics.com/course/eukaryotic-metabarcoding-eukb01/
Oliver Hooker PhD.
PR statistics
2017 publications -
Ecosystem size predicts eco-morphological variability in post-glacial
diversification. Ecology and Evolution. In press.
The physiological costs of prey switching reinforce foraging
specialization. Journal of animal ecology.
prstatistics.com
facebook.com/prstatistics/
twitter.com/PRstatistics
groups.google.com/d/forum/pr-statistics-post-course-forum
prstatistics.com/organiser/oliver-hooker/
6 Hope Park Crescent
Edinburgh
EH8 9NA
+44 (0) 7966500340
--
Oliver Hooker PhD.
PR statistics
2017 publications -
Ecosystem size predicts eco-morphological variability in post-glacial
diversification. Ecology and Evolution. In press.
The physiological costs of prey switching reinforce foraging
specialization. Journal of animal ecology.
prstatistics.com
facebook.com/prstatistics/
twitter.com/PRstatistics
groups.google.com/d/forum/pr-statistics-post-course-forum
prstatistics.com/organiser/oliver-hooker/
6 Hope Park Crescent
Edinburgh
EH8 9NA
+44 (0) 7966500340
--
Oliver Hooker PhD.
PR statistics
2017 publications -
Ecosystem size predicts eco-morphological variability in post-glacial
diversification. Ecology and Evolution. In press.
The physiological costs of prey switching reinforce foraging
specialization. Journal of animal ecology.
prstatistics.com
facebook.com/prstatistics/
twitter.com/PRstatistics
groups.google.com/d/forum/pr-statistics-post-course-forum
prstatistics.com/organiser/oliver-hooker/
6 Hope Park Crescent
Edinburgh
EH8 9NA
+44 (0) 7966500340
More information about the R-sig-genetics
mailing list