DNA sequence polymorphism analysis using DnaSP

Methods in Molecular Biology

Volumn 537, Issue , 2009, Pages 337-350

  Rozas, Julio ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

Author keywords

Coalescent methods; DNA sequence polymorphisms; DnaSP; Molecular population genetics software; SNPs, Neutrality tests

Indexed keywords

ARTICLE; BIOLOGY; COMPUTER INTERFACE; COMPUTER PROGRAM; DNA SEQUENCE; GENETIC POLYMORPHISM; GENETICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; POLYMORPHISM, GENETIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 68049133091     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-251-9_17     Document Type: Article

References (30)

1. Przeworski, M., Hudson, R. R., and Di Rienzo, A. (2000) Adjusting the focus on human variation. Trends Genet 16, 296-302. (Pubitemid 30389601)
2. Nordborg, M., and Innan, H. (2002) Molecular population genetics.Curr Opin Plant Biol 5, 69-73. (Pubitemid 34060481)
3. Rosenberg, N. A., and Nordborg, M. (2002) Genealogical trees, coalescent theory, and the analysis of genetic polymorphisms. Nat Rev Genet 3, 380-90. (Pubitemid 34506719)
4. Hudson, R. R. (1990) Gene genealogies and the coalescent process, in Oxford Surveys in Evolutionary Biology (Futuyma, D. J., and Antonovics, J. D., Eds.), Oxford University Press, New York. pp. 1-44.
5. Excoffier, L., and Heckel, G. (2006) Computer programs for population genetics data analysis: a survival guide. Nat Rev Genet 7, 745-58. (Pubitemid 44413219)
6. Rozas, J., Sánchez-DelBarrio, J. C., Messe-guer, X., and Rozas, R. (2003) DnaSP, DNA polymorphism analyses by the coales-cent and other methods. Bioinformatics 19, 2496-7. (Pubitemid 38016658)
7. Rozas, J., and Rozas, R. (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15, 174-5. (Pubitemid 29134733)
8. Excoffier, L., Laval, G., and Schneider, S. (2005) Arlequin (version 3): An integrated software package for population genetics data analysis.Evol Bioinf Online 1, 47-50.
9. Bandelt, H.-J., Forster, P., and Röhl, A. (1999) Median-Joining networks for infer ring intraspecific phylogenies. Mol Biol Evol 16, 37-48. (Pubitemid 29024937)
10. Maddison, W. P., Swofford, D. L., and Maddison, D. R. (1997) NEXUS: an extendible file format for systematic information. Syst Biol 46, 590-621.
11. Maddison, D. R., and Maddison, W. P. (2000) MacClade 4, version 4. Sinauer, Sunderland, MA.
12. Swofford, D. L. (1998) PAUP*. Phylogenetic Analysis Using Parsimony (*and other Methods). Sinauer Associates, Sunderland, MA.
13. Kumar, S., Tamura, K., and Nei, M. (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinf 5, 150-63.
14. Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
15. Jukes, T. H., and Cantor, C. R. (1969) Evolution of protein molecules, in Mammalian Protein Metabolism (Munro, H. N. Ed.), Academic Press, New York, pp. 21-132.
16. Stephens, M., and Donnelly, P. (2003) A comparison of bayesian methods for hap-lotype reconstruction from population genotype data. Am J Hum Genet 73, 1162-9. (Pubitemid 37414228)
17. Slatkin, M., and Hudson, R. R. (1991) Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129, 555-62.
18. Rogers, A. R., and Harpending, H. (1992) Population growth makes waves in the distribution of pairwise genetic differences.Mol Biol Evol 9, 552-69.
19. Ramos-Onsins, S. E., and Rozas, J. (2002) Statistical properties of new neutrality tests against population growth. Mol Biol Evol 19, 2092-100. (Pubitemid 35440445)
20. Harpending, H.(1994) Signature ofancient population growth in alow-resolution mito-chondrial DNA mismatch distribution. Hum Biol 66, 591-600. (Pubitemid 2117524)
21. Mcdonald, J. H., and Kreitman, M. (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351, 652-4. (Pubitemid 21896661)
22. Yang, Z., and Bielawski, J. P. (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15, 496-503.
23. Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-95. (Pubitemid 19274682)
24. Fu, Y.-X., and Li, W.-H. (1993) Statistical tests of neutrality of mutations. Genetics 133, 693-709. (Pubitemid 23066572)
25. Hudson, R. R., Kreitman M., and Aguadé, M. (1987) A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153-9.
26. Fay, J. C., and Wu, C. I. (2000) Hitchhiking under positive darwinian selection. Genetics 155, 1405-13. (Pubitemid 30463447)
27. Hutter, S., Vilella, A, J., and Rozas, J. (2006) Genome-wide DNA polymorphism analyses using VariScan. BMC Bioinf 7, 409.
28. Nordborg, M. (2001) Coalescent theory, in Handbook of Statistical Genetics (En Balding, D., Bishop, M., and Cannings, C., Eds.), John Wiley & Sons, Chichester, pp. 179-212.
29. Rozas, J., Segarra, C., Ribó, G., and Aguadé, M. (1999) Molecular population genetics of the rp49gene region in different chromosomal inversions of Drosophila sub-obscura. Genetics 151, 189-202. (Pubitemid 29031887)
30. Rogers, A. R. (1995) Genetic evidence for a Pleistocene population explosion. Evolution 49, 608-15.