ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
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.