tools for identifying population structure

fastIBD would be more computational workable. 


(1) ERSA
Maximum-likelihood estimation of recent shared ancestry (ERSA).
Huff C*, Witherspoon DJ*, Simonson T, Xing J, Watkins S, Zhang Y, Tuohy T, Neklason D, Burt R, Guthery S, Woodward S, Jorde LB. Genome Res. 2011 Feb 8.

(2) germline
Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe'er I (2008) Whole population, genomewide mapping of hidden relatedness. Genome Research.

(3) fineSTRUCTRUE/paintingmychromosomes
Lawson, Hellenthal, Myers, and Falush (In Press), "Inference ofpopulation structure using dense haplotype data", PLoSGenetics. (preprint, Supporting Information).

(4) fastIBD/beagle

1. BEAGLE's fastIBD method is described in

   B L Browning and S R Browning (2011)  A fast, powerful method for detecting identity by descent.  The American Journal of Human Genetics 88:173-182.  [link to article]
   

2. BEAGLE's methods for detecting homozygosity-by-descent and identity-by-descent are described in

   S R Browning and B L Browning (2010)  High-resolution detection of identity by descent in unrelated individuals.   The American Journal of Human Genetics 86:526-539. [link to article] 

3. BEAGLE's methods for calling genotypes from genotype likelihood data are described in

   B L Browning and Z Yu (2009)  Simultaneous genotype calling and haplotype phase inference improves genotype accuracy and reduces false positive associations for genome-wide association studies.   The American Journal of Human Genetics 85:847-861. [link to article] 

4. BEAGLE's methods for imputing ungenotyped markers and phasing parent-offspring trios are described in

   B L Browning and S R Browning (2009) A unified approach to genotype imputation and haplotype phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet 84:210-223. [link to article]

5. BEAGLE's methods for inferring haplotype phase or sporadic missing data in unrelated individuals are described in

   S R Browning and B L Browning (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies using localized haplotype clustering. Am J Hum Genet 81:1084-1097. [link to article]

6. BEAGLE's methods for association testing are described in

   B L Browning and S R Browning (2007) Efficient multilocus association mapping for whole genome association studies using localized haplotypeclustering. Genet Epidemiol 31:365-375. [link to article]

7. BEAGLE's haplotype frequency model was first described in:
   

   S R Browning (2006) Multilocus association mapping using variable-length Markov chains. Am J Hum Genet 78:903-13. [link to article] 

(5) Comparison of MCLUST with fineSTRUCTURE