"Phylogenetic data analysis using R" Many people studying morphology and the evolution of shape will find their research often overlaps in to the field of phylogeny.
FINAL CALL - LAST FEW PLACES Delivered by Dr. Emmanuel Paradis *www.prstatistics.com/course/introduction-to-phylogenetic-analysis-with-r-phyg-phyl02/* <http://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 oliverhoo...@prstatistics.com or visit our website *www.prstatistics.com* <http://www.prstatistics.com/> Please feel free to distribute this material anywhere you feel is suitable PRstatistics upcoming courses - email for details oliverhoo...@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/* <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/* <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/* <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/* <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/* <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/* <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/* <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/* <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/* <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/* <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/* <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/* <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/* <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/* <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/* <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/* <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/* <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/* <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/* <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/* <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* <http://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* <http://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* <http://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/* <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/* <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/* <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/* <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 -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. 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