McKenna, MC, Bell, SK & Simpson, GG. (1997) Classification of Mammals Above the Species Level (Columbia Univ Press, New York,).
Lecointre, G & Le Guyader, H. (2006) The Tree of Life: A Phylogenetic Classification (Belknap Press of Harvard Univ Press, Cambridge, MA,).
Donoghue, MJ & Cracraft, J. (2004) in Assembling the Tree of Life eds. Cracraft, J & Donoghue, MJ. (Oxford Univ Press, Oxford, UK,) pp. 1–4.
Cannarozzi, G, Schneider, A & Gonnet, G. (2007) PLoS Comput Biol 3, e2
Douady, CJ, Chatelier, PI, Madsen, O, de Jong, WW, Catzeflis, F, Springer, MS & Stanhope, MJ. (2002) Mol Phylogenet Evol 25, 200–209
Huttley, GA, Wakefield, MJ & Easteal, S. (2007) Mol Biol Evol 24, 1702–1730
Kullberg, M, Nilsson, MA, Arnason, U, Harley, EH & Janke, A. (2006) Mol Biol Evol 23, 1493–1503
Misawa, K & Nei, M. (2003) J Mol Evol 57, Suppl 1, S290–S296
Murphy, WJ, Eizirik, E, O'Brien, SJ, Madsen, O, Scally, M, Douady, CJ, Teeling, E, Ryder, OA, Stanhope, MJ & de Jong, WW, et al. (2001) Science 294, 2348–2351
Nikolaev, S, Montoya-Burgos, JI, Margulies, EH, Program, NC, Rougemont, J, Nyffeler, B & Antonarakis, SE. (2007) PLoS Genet 3, e2
van Rheede, T, Bastiaans, T, Boone, DN, Hedges, SB, de Jong, WW & Madsen, O. (2006) Mol Biol Evol 23, 587–597
de Jong, WW, van Dijk, MAM, Poux, C, Kappe, G, van Rheede, T & Madsen, O. (2003) Mol Phylogenet Evol 28, 328–340
Kriegs, JO, Churakov, G, Kiefmann, M, Jordan, U, Brosius, J & Schmitz, J. (2006) PLoS Biol 4, e91
Murphy, WJ, Pringle, TH, Crider, TA, Springer, MS & Miller, W. (2007) Genome Res 17, 413–421.
Nishihara, H, Hasegawa, M & Okada, N. (2006) Proc Natl Acad Sci USA 103, 9929–9934
Asher, RJ. (2005) in The Rise of Placental Mammals: Origins and Relationships of the Major Extant Clades eds. Rose, KD & Archibald, JD. (Johns Hopkins Univ Press, Baltimore, MD,) pp. 50–70.
Waters, PD, Dobigny, G, Waddell, PJ & Robinson, TJ. (2007) PLoS ONE 2, e158
Felsenstein, J. (2004) Inferring Phylogenies (Sinauer, Sunderland, MA,).
Kolaczkowski, B & Thornton, JW. (2004) Nature 431, 980–984
Bailey, WJ, Fitch, DH, Tagle, DA, Czelusniak, J, Slightom, JL & Goodman, M. (1991) Mol Biol Evol 8, 155–184
Elango, N, Thomas, JW & Yi, SV. (2006) Proc Natl Acad Sci USA 103, 1370–1375.
Delsuc, F, Brinkmann, H & Philippe, H. (2005) Nat Rev 6, 361–375
Felsenstein, J. (1985) Evolution (Lawrence, Kans) 39, 783–791.
Jeffroy, O, Brinkmann, H, Delsuc, F & Philippe, H. (2006) Trends Genet 22, 225–231
Nei, M & Kumar, S. (2000) Molecular Evolution and Phylogenetics (Oxford Univ Press, Oxford,).
Yang, Z. (2006) Computational Molecular Evolution (Oxford Univ Press, Oxford,).
Phillips, MJ, Delsuc, F & Penny, D. (2004) Mol Biol Evol 21, 1455–1458
Felsenstein, J. (1978) Syst Zool 27, 401–410.
Springer, MS, Stanhope, MJ, Madsen, O & de Jong, WW. (2004) Trends Ecol Evol 19, 430–438
Inagaki, Y, Susko, E, Fast, NM & Roger, AJ. (2004) Mol Biol Evol 21, 1340–1349
Lockhart, PJ, Larkum, AW, Steel, M, Waddell, PJ & Penny, D. (1996) Proc Natl Acad Sci USA 93, 1930–1934
Brown, JH & Lomolino, MV. (1998) Biogeography (Sinauer, Sunderland, MA,).
Springer, MS, Murphy, WJ, Eizirik, E & O'Brien, SJ. (2003) Proc Natl Acad Sci USA 100, 1056–1061
Altschul, SF, Gish, W, Miller, W, Myers, EW & Lipman, DJ. (1990) J Mol Biol 215, 403–410
Thompson, JD, Higgins, DG & Gibson, TJ. (1994) Nucleic Acids Res 22, 4673–4680
Lander, ES, Linton, LM, Birren, B, Nusbaum, C, Zody, MC, Baldwin, J, Devon, K, Dewar, K, Doyle, M. & FitzHugh, W, et al. (2001) Nature 409, 860–921
The Chimpanzee Sequencing and Analysis Consortium (2005) Nature 437, 69–87
Gibbs, RA, Rogers, J, Katze, MG, Bumgarner, R, Weinstock, GM, Mardis, ER, Remington, KA, Strausberg, RL, Venter, JC & Wilson, RK, et al. (2007) Science 316, 222–234
Waterston, RH, Lindblad-Toh, K, Birney, E, Rogers, J, Abril, JF, Agarwal, P, Agarwala, R, Ainscough, R, Alexandersson, M & An, P, et al. (2002) Nature 420, 520–562
Gibbs, RA, Weinstock, GM, Metzker, ML, Muzny, DM, Sodergren, EJ, Scherer, S, Scott, G, Steffen, D, Worley, KC & Burch, PE, et al. (2004) Nature 428, 493–521
Lindblad-Toh, K, Wade, CM, Mikkelsen, TS, Karlsson, EK, Jaffe, DB, Kamal, M, Clamp, M, Chang, JL, Kulbokas, EJ III & Zody, MC, et al. (2005) Nature 438, 803–819
Mikkelsen, TS, Wakefield, MJ, Aken, B, Amemiya, CT, Chang, JL, Duke, S, Garber, M, Gentles, AJ, Goodstadt, L & Heger, A, et al. (2007) Nature 447, 167–177
International Chicken Genome Sequencing Consortium (2004) Nature 432, 695–716
Tamura, K, Dudley, J, Nei, M & Kumar, S. (2007) Mol Biol Evol 24, 1596–1599
Swofford, DL. (2002) PAUP*: Phylogenetic Analysis Using Parsimony* (and Other Methods) (Sinauer, Sunderland, MA,).
Posada, D & Crandall, KA. (1998) Bioinformatics 14, 817–818.
Guindon, S & Gascuel, O. (2003) Syst Biol 52, 696–704
Hordijk, W & Gascuel, O. (2005) Bioinformatics 21, 4338–4347
Altekar, G, Dwarkadas, S, Huelsenbeck, JP & Ronquist, F. (2004) Bioinformatics 20, 407–415
Huelsenbeck, JP & Ronquist, F. (2001) Bioinformatics 17, 754–755
Ronquist, F & Huelsenbeck, JP. (2003) Bioinformatics 19, 1572–1574
Pagel, M & Meade, A. (2004) Syst Biol 53, 571–581
Cox, CB, Healey, IN & Moore, PD. (1976) Biogeography: An Ecological and Evolutionary Approach (Wiley, New York,).
Liu, G, Uddin, M, Islam, M, Goodman, M, Grossman, LI, Romero, R & Wildman, DE. (2007) Source Code Med Biol in press.
Answers to all your Biology Questions
