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Orlando2013
Orlando, L, Ginolhac, A, Zhang, G, Froese, D, Albrechtsen, A, Stiller, M, Schubert, M, Cappellini, E, Petersen, B, Moltke, I, Johnson, PL, Fumagalli, M, Vilstrup, JT, Raghavan, M, Korneliussen, T, Malaspinas, AS, Vogt, J, Szklarczyk, D, Kelstrup, CD, Vinther, J, Dolocan, A, Stenderup, J, Velazquez, AM, Cahill, J, Rasmussen, M, Wang, X, Min, J, Zazula, GD, Seguin-Orlando, A, Mortensen, C, Magnussen, K, Thompson, JF, Weinstock, J, Gregersen, K, Røed, KH, Eisenmann, V, Rubin, CJ, Miller, DC, Antczak, DF, Bertelsen, MF, Brunak, S, Al-Rasheid, KA, Ryder, O, Andersson, L, Mundy, J, Krogh, A, Gilbert, MT, Kjær, K, Sicheritz-Ponten, T, Jensen, LJ, Olsen, JV, Hofreiter, M, Nielsen, R, Shapiro, B, Wang, J, Willerslev, E (2013). Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature, 499, 7456:74-8.
Pages
Population genetics
Population structure
- Admixture
- Fst
- ABBABABA (D-stat)
- ABBABABA (multipop)
- Population branch statistics (pbs)
- PCA
- PCA (sampling approach)
- Linkage disequilibrium
Medical genetics
IBD/IBS
Summaries
SNPs and genotypes
- Genotypes likelihoods
- Major and Minor
- Allele frequencies
- Genotype calling
- Haploid calling
- SNP Calling
Output
Misc/util programs
Program structure
About ANGSD