POPBAM: Tools for evolutionary analysis of short read sequence alignments

Evolutionary Bioinformatics

Volumn 2013, Issue 9, 2013, Pages 343-353

  Garrigan, Daniel ^a  

^a UNIVERSITY OF ROCHESTER   (United States)

Author keywords

Divergence; Linkage disequilibrium; Natural selection; Next generation sequencing; Polymorphism

Indexed keywords

ACCURACY; ARTICLE; BIOINFORMATICS; CHROMOSOME; COMPUTER LANGUAGE; COMPUTER PROGRAM; FEASIBILITY STUDY; GENE LINKAGE DISEQUILIBRIUM; GENETIC VARIABILITY; GENOME ANALYSIS; INTERNET; MOLECULAR EVOLUTION; MUTATION RATE; NATURAL SELECTION; NONHUMAN; PHYLOGENETIC TREE; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84883613924     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: 10.4137/EBO.S12751     Document Type: Article

References (42)

1. Cao J, Schneeberger K, Ossowski S, etal. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet. 2011;43:956-63.
2. Ellegren H, Smeds L, Burri R, etal. The genomic landscape of species divergence in Ficedula flycatchers. Nature. 2012;491:756-60.
3. Garrigan D, Kingan SB, Geneva AJ, etal. Genome sequencing reveals complex speciation in the Drosophila simulans clade. Genome Res. 2012;22:1499-511.
4. Jones FC, Grabherr MG, Chan YF, etal. The genomic basis of adaptive evolution in threespine sticklebacks. Nature. 2012;484:55-61.
5. Mackay TFC, Richards S, Stone EA, etal. The Drosophila melanogaster genetic reference panel. Nature. 2012;482:173-8.
6. Li H, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform. 2010;11:473-83.
7. Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics. 2010;95:315-27.
8. Kim J, Larkin DM, Cai Q, etal. Reference-assisted chromosome assembly. Proc Natl Acad Sci U S A. 2013;110:1785-90.
9. Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet. 2012;13:36-46.
10. Nielsen R, Paul JS, Albrechsten A, Song YS. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet. 2011;12:443-51.
11. Aguiar D, Istrail S. HapCompass: a fast cycle basis algorithm for accurate haplotype assembly of sequence data. J Comput Biol. 2012;19:577-90.
12. Sousa V, Hey J. Understanding the origin of species with genome-scale data: modelling gene flow. Nat Rev Genet. 2013;14:404-14.
13. International Organization for Standardization. Information technology-Programming languages-C++. ISO/IEC 14882:2011.
14. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6. 2005. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
15. Li H, Handsaker B, Wysoker A, etal. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078-9.
16. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008;18:1851-8.
17. Ewing B, Green P. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 1998;8:186-94.
18. Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2010;38:1767-71.
19. Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C. Genomic scans for selective sweeps using SNP data. Genome Res. 2005;15: 1566-75.
20. Hudson RR. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics. 2002;18:337-8.
21. Thornton K. Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics. 2003;19:2325-7.
22. Nei M, Tajima F. DNA polymorphism detectable by restriction endonucleases. Genetics. 1981;97:145-63.
23. Tang K, Thornton KR, Stoneking M. A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol. 2007;5:e171.
24. Nei M, Roychoudhury AK. Sampling variance of heterozygosity and genetic distance. Genetics. 1974;74:371-80.
25. Geneva AJ, Muirhead CA, Lovato LM, Kingan SB, Garrigan D. A simple statistic to detect recent gene flow from whole-genome data. Genetics. 2013.
26. Kelly JK. A test of neutrality based on interlocus associations. Genetics. 1997;146:1197-206.
27. Kim Y, Nielsen R. Linkage disequilibrium as a signature of selective sweeps. Genetics. 2004;167:1513-24.
28. Wall JD. Recombination and the power of statistical tests of neutrality. Genet Res. 1999;74:65-79.
29. Nei M, Li W-H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A. 1979;76:5269-73.
30. Hudson RR, Slatkin M, Maddison WP. Estimation of levels of gene flow from DNA sequence data. Genetics. 1992;132:583-9.
31. Jukes TH, Cantor CR. Evolution of protein molecules. In Mammalian Protein Metabolism, III (Munro HN, editor) New York: Academy Press; 1969.
32. Hudson RR, Kreitman M, Aguadé M. A test of neutral molecular evolution based on nucleotide data. Genetics. 1987;116:153-9.
33. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406-25.
34. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123:585-95.
35. Tajima F. Estimation of the amount of DNA polymorphism and statistical tests of the neutral mutation hypothesis based on DNA polymorphism. In Progress in Population Genetics and Human Evolution (Donnelly P, Tavaré S, editors) New York: Springer; 1997.
36. Fay JC, Wu C-I. Hitchhiking under positive Darwinian selection. Genetics. 2000;155:1405-13.
37. Zeng K, Fu Y-X, Shi S, Wu C-I. Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics. 2006;174:1431-9.
38. Watterson GA. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 1975;7:256-76.
39. R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing Vienna, Austria 2013.
40. Pool JE, Corbett-Detig RB, Sugino RP, etal. Population genomics of sub-Saharan Drosophila melanogaster: African diversity and non-African admixture. PLoS Genet. 2012;8:e1003080.
41. Danecek P, Auton A, Abecasis G, etal. The variant call format and VCFtools. Bioinformatics. 2011;27:2156-8.
42. Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25:1451-2.