SNPGenie: Estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data

Bioinformatics

Volumn 31, Issue 22, 2015, Pages 3709-3711

  Nelson, Chase W ^a   Moncla, Louise H ^b   Hughes, Austin L ^a  

^a UNIVERSITY OF SOUTH CAROLINA   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEMAGGLUTININ; SIALIDASE;

EVOLUTION; GENETIC SELECTION; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INFLUENZA A VIRUS (H5N1); POPULATION GENETICS; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; SOFTWARE;

BIOLOGICAL EVOLUTION; GENETICS, POPULATION; HEMAGGLUTININS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFLUENZA A VIRUS, H5N1 SUBTYPE; NEURAMINIDASE; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC; SOFTWARE;

EID: 84947773762     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv449     Document Type: Article

References (14)

1. Cutler,D.J. and Jensen,J.D. (2010) To pool, or not to pool? Genetics, 186, 41-43.
2. Futschik,A. and Schlötterer,C. (2010) The next generation of molecular markers from massively parallel sequencing of pooled DNA samples. Genetics, 186, 207-218.
3. Graur,D. and Li,W.-H. (2000) Fundamentals of Molecular Evolution, 2nd Ed., Sinauer Associates, Inc., Sunderland, MA.
4. Hughes,A.L. (1999) Adaptive Evolution of Genes and Genomes, Oxford University Press, New York.
5. Hughes,A.L. et al. (2011) Widespread purifying selection at polymorphic sites in human protein-coding loci. Proc. Natl. Acad. Sci. USA, 100, 15754-15757.
6. Knapp,E.W. et al. (2011) PolyAna: analyzing synonymous and nonsynonymous polymorphic sites. Conserv. Genet. Resourc., 3, 429-431.
7. Kofler,R. et al. (2011) PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals. PLoS One, 6, e15925.
8. Lynch,M. et al. (2014) Population-genetic inference from pooled-sequencing data. Genome Biol. Evol., 6, 1210-1218.
9. Nei,M. (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
10. Nei,M. and Gojobori,T. (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol., 3, 418-426.
11. Nelson,C.W. and Hughes,A.L. (2015) Within-host nucleotide diversity of virus populations: Insights from next-generation sequencing. Infect. Genet. Evol., 30, 1-7.
12. Raineri,E. et al. (2012) SNP calling by sequencing pooled samples. BMC Bioinformatics, 13, 239.
13. Tamura,K. et al. (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol., 30, 2725-2729.
14. Wilker,P.R. et al. (2013) Selection on haemagglutinin imposes a bottleneck during mammalian transmission of reassortant H5N1 influenza viruses. Nat. Commun., 4, 2636.