In parallel to the main program, two workshops exploring the use of the BEAST and GenAlEx program packages will be held on the 14th of July. The workshops will be held in computer labs G08 and G11 on the ground floor of the Biological Sciences Building (D26), located in the upper campus area near Gate 11 Botany Street. A map of the campus is available at http://www.facilities.unsw.edu.au/getting-uni/campus-maps .
Registration for these is free. Places will be allocated on a first-registered basis as numbers are limited to 40. Owing to this, at most two members of the same research group can be accommodated. Lunch will not be provided at the workshops but can be bought at nearby venues on the campus.
Proposed workshop programmes:
Course offered by Dr Simon Ho of the Molecular Ecology, Evolution, and Phylogenetics group in the School of Biological Sciencws of the University of Sydney.
9.30-10.00: Lecture: Introduction to Phylogenetic Analysis
10.00-10.45: Lecture: Phylogenetic Methods
11.00-13.00: Practical: The evolution of ratite birds
14.00-15.30: Lecture: Bayesian Phylogenetic Analysis
15.30-17.30: Practical: A mysterious hominin from Siberia
An introduction to GenAlEx: Genetic Analysis in Excel
Course offered by Rod Peakall, Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra ACT 0022
GenAlEx 6.5 offers a wide range of population genetic analysis options for the full spectrum of genetic markers within the Microsoft Excel environment on both PC and Macintosh computers. When combined with its user-friendly interface, rich graphical outputs for data exploration and publication, tools for data manipulation and export options to many other software packages, we believe that GenAlEx offers an ideal launching pad for population genetic analysis by students, teachers and researchers alike (Peakall and Smouse 2012).
This full day workshop on GenAlEx begins at 9.30. It will introduce participants to this genetics package and provide hands on experience in the operation of the software. No prior experience with software is required. However, participants are expected to be familiar with modern DNA based genetic markers, and general aspects of population genetic analysis. Some prior experience with Excel is desirable. Participants are also encouraged to bring their own genetic data for analysis in the final session.
The workshop consists of 4 modules as follows:
Module 1: Introduction to GenAlEx
This module will commence with an overview of the capabilities of GenAlEx. Next users will be given hands-on training in the basic operation of the software including data formats and parameters.
Module 2: Operating GenAlEx
The analysis options in GenAlEx are broadly subdivided into frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation). This module will introduce participants to both analysis options, drawing on real data examples to illustrate the process involved.
Module 3: Getting the most out of GenAlEx
This module will introduce participants to some of the many useful features of GenAlEx including data import and export, and a host of other useful functions that will enhance your use of Excel generally.
Module 4: Real data analysis in GenAlEx
This module will give participants the opportunity to begin working with their own datasets. For those that don’t have there own data, we will provide multiple examples of real data sets.
GenAlEx – Genetic Analysis in Excel (Peakall and Smouse 2006, 2012) is designed as a user-friendly package with an intuitive and consistent interface that allows users to analyse a wide range of population genetic data within a software environment with which most users will have some familiarity (MS Excel). GenAlEx is now widely used by university teachers at both undergraduate and graduate levels in Australia, North America, South America, and Europe. The software also offers a wide range of analysis options for researchers, including some spatial analysis options not available elsewhere. More than 6000 registered users, representing over 60 countries, have used the software. According to ISI, the first paper describing the software was cited more than 2500 times in the period 2006 to 2012.
GenAlEx offers analysis of codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. GenAlEx 6.5 (released in 2012) offers new features including calculation of new estimators of population structure: GST, Jost’s Dest, and FST via AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data, and heterogeneity tests for spatial autocorrelation analysis. Data export is provided to more than 30 other software packages.
Peakall, R. and Smouse P.E. (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics 28, 2537-2539. Freely available as an open access article from: http://bioinformatics.oxfordjournals.org/content/28/19/2537
Peakall, R. and Smouse P.E. (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes. 6, 288-295.
The software and supporting documentation is freely available from The Australian National University, Canberra, Australia: http://biology.anu.edu.au/GenAlEx