Jpopgen suite: Population genetic analysis of DNA polymorphism from nucleotide sequences with errors

Methods in Ecology and Evolution

Volumn 3, Issue 4, 2012, Pages 624-627

  Liu, Xiaoming ^a  

^a UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

Neutrality test; Next generation sequencing; Population genetics; Population growth rate; Population mutation rate; Sequencing error

Indexed keywords

EID: 84886090615     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/j.2041-210X.2012.00194.x     Document Type: Article

References (20)

1. Achaz, G. (2008) Testing for neutrality in samples with sequencing errors Genetics, 179, 1409-1424
2. Achaz, G. (2009) Frequency spectrum neutrality tests: one for all and all for one. Genetics, 183, 249-258
3. Fay, J.C. & Wu, C.I. (2000) Hitchhiking under positive Darwinian selection Genetics, 155, 1405-1413
4. Fu, Y.X. (1994) Estimating effective population size or mutation rate using the frequencies of mutations of various classes in a sample of DNA sequences Genetics, 138, 1375-1386
5. Fu, Y.X.&Li, W.H. (1993) Statistical tests of neutrality of mutations. Genetics, 133, 693-709
6. Hellmann, I., Mang, Y., Gu, Z., Li, P., de la Vega, F.M., Clark, A.G. & Nielsen, R. (2008) Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Research, 18, 1020-1029
7. Hudson, R.R. (2002)Generating samples under aWright-Fisher neutral model of genetic variation. Bioinformatics, 18, 337-338
8. Johnson, P.L.F. & Slatkin,M. (2006) Inference of population genetic parameters in metagenomics: a clean look at messy data. Genome Research, 16, 1320-1327
9. Johnson, P.L.F. & Slatkin, M. (2008) Accounting for bias from sequencing error in population genetic estimates. Molecular Biology and Evolution, 25, 199-206
10. Johnson, P.L.F. & Slatkin, M. (2009) Inference of microbial recombination rates from metagenomic data. PLoS Genetics, 5, e1000674
11. Knudsen, B. & Miyamoto, M.M. (2007) Incorporating experimental design and error into coalescent / mutation models of population history. Genetics, 176, 2335-2342
12. Knudsen, B. & Miyamoto, M. (2009) Accurate and fast methods to estimate the population mutation rate from error prone sequences. BMC Bioinformatics, 10, 247
13. Liu, X., Maxwell, T.J., Boerwinkle, E. & Fu, Y.X. (2009) Inferring population mutation rate and sequencing error rate using the SNP frequency spectrum in a sample of DNA sequences. Molecular Biology and Evolution, 26, 1479-1490
14. Liu, X., Fu, Y.X., Maxwell, T.J. & Boerwinkle, E. (2010) Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error. Genome Research, 20, 101-109
15. Lynch,M. (2009) Estimation of allele frequencies from high-coverage genomesequencing projects. Genetics, 182, 295-301
16. Shendure, J.&Ji,H. (2008)Next-generationDNAsequencing. Nature Biotechnology, 26, 1135-1145
17. Tajima, F. (1983) Evolutionary relationship of DNA-sequences in finite populations Genetics, 105, 437-460
18. Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis byDNApolymorphism. Genetics, 123, 585-595
19. Watterson, G.A. (1975) Number of segregating sites in genetic models without recombination. Theoretical Population Biology, 7, 256-276
20. Zeng, K., Fu, Y.X., Shi, S. & Wu, C.I. (2006) Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics, 174, 1431-1439