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GenAlEx  

2012-10-01 22:11:39|  分类: 生物信息编程 |  标签: |举报 |字号 订阅

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http://biology.anu.edu.au/GenAlEx/Tutorials.html
GenAlEx: Genetic Analysis in Excel is a popular cross platform package for population genetic analysis that runs within Microsoft Excel. 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. In GenAlEx 6.5 we introduce exciting new features including calculation of new estimators of population structure: G’ST, G’’ST, Jost’s Dest, and F’ST 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. New teaching tutorials and extra step-by-step options are also included. The comprehensive independently written guide has been fully revised

Tutorial 1 (zip 6.9 mb) 

An Introduction to Frequency-Based Population Genetic Analysis: scoring genetic markers, Allele Frequency, Heterozygosity, F-statistics, Nei Genetic Distance, Shannon Diversity Indices and Chi-square tests for Hardy-Weinberg Equilibrium

Tutorial 2 (zip 1.3 mb) 

Genetic Distance and AMOVA: Haploid, Codominant and Binary Genetic Distance,AMOVA and F-statistics

Tutorial 3 (zip 4.5 mb)

Spatial Genetic Analysis: Principal Coordinate Analysis (PCoA), Mantel Tests for Matrix Correspondence and Spatial Autocorrelation Analysis

Tutorial 4 (zip 2.6 mb)

Advanced Frequency-Based Analysis: DNA Profile Probability, Probability of Identity, Probability of Exclusion, Population Assignment and Pairwise Relatedness

Tutorial 5 (zip 2 mb)

Advanced Features Including Data Import and Export: Working with DNA sequences, importing and processing raw genotypic data, exporting data from GenAlEx to other software. The Stats menu and how to customise the GenAlEx menu are also covered briefly.

Tutorial 6 (zip 1 mb)

TwoGener: Male gametic inference, male gametic distances, gametic AMOVA


Coming soon - New tutorials outlining some of the new features in GenAlEx 6.5

Tutorial 7:

New estimators of population genetic structure:  G’ST, G’’ST and Jost’s Dest, and standardized F’ST via AMOVA

Tutorial 8:

Pairwise Linkage Disequilibrium: estimation of D, D’, r, and r2 for biallelic markers

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