User:Dbeatty/Sandbox
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| Species: | Z. mays
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| Zea mays | |
Association Mapping (or LD Mapping )
Background
[edit]Population structure can lead to false positives. GC - Gas Chromotography
Software
[edit]- Affeymetrix LD (C/C++)
- FASTLINK (C - last updated 1999?)
- Software for Linkage and Mapping
- PyPop (Python/C)
- Haploview (Java)
- Software from Broad Institute (that may or may not be helpful)
- MERLIN (Linkage, Parametric Linkage, IBD Estimation, Regression, LD, Association Analysis) (C++)
- LAMP (Linkage and Association Modeling in Pedigrees - uses maximum likelihood model) (C++)
- All Software from BIO 666
- Association Mapping Software (including MCMC, HapCluster, and Block-Association Mapping)
- SPAGeDi (Spatial Pattern Analysis of Genetic Diversity - primarily designed to characterize the spatial genetic structure of mapped individuals and/or mapped populations using genotype data of any ploidy level.)
- TASSEL (is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.)
- Structure (is a free software package for using multi-locus genotype data to investigate population structure.)
- STRAT (is a companion program to structure. It is written for use in association mapping, enabling valid case-control studies even in the presence of population structure.)
- Links to software from STATISTICAL GENETICS: Gene Mapping Through Linkage and Association textbook
Linkage Disequilibrium Measures
[edit]- correlation coefficient delta (Hill and Robertson 1968)
- Lewontin's D' (range constrained by allele frequencies 1964)
- robust formulation of the population attributable risk delta
- Yule's Q
- Kaplan and Weir's proportional difference d under the assumption of complete disequalibrium between disease and marker loci
Maize Websites
[edit]- Edward Buckler's Maize Lab
- Molecular and Functional Diversity of the Maize Genome
- MaizeGDB - Maize Genetics and Genomics Database
- Maize Mapping Project
- The TIGR Maize Database
Maize Markers
[edit]- MaizeGDB - 2018 SSR
Lecture Notes
[edit]- Hardy Weinberg Equilibrium
- Linkage Disequalibrium
- Haplotyping
- Haplotype Based Association Tests
- IBS Methods for Affected Pairs Linkage
Terms and Phrases
[edit]- SNP (Single Nucleotide Polymorphism)
- Linkage
- Linkage Disequalibrium
- Association Mapping
- Association Mapping slides (129 pages)
- Coalescent theory for LD mapping
- Markov Chain Monte Carlo (MCMC)
- Recombination
- Haplotype
- Hardy Weinberg principle
References
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Credit:
(see original file).
