Processing and population genetic analysis of multigenic datasets with ProSeq3 software

Bioinformatics

Volumn 25, Issue 23, 2009, Pages 3189-3190

  Filatov, Dmitry A ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGY; COMPUTER PROGRAM; DNA SEQUENCE; ETHNIC AND RACIAL GROUPS; GENETIC POLYMORPHISM; GENETICS; HUMAN; METHODOLOGY; POPULATION GENETICS; SEQUENCE ALIGNMENT;

COMPUTATIONAL BIOLOGY; GENETICS, POPULATION; HUMANS; POLYMORPHISM, GENETIC; POPULATION GROUPS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 75949124473     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp572     Document Type: Article

References (17)

1. Begun, D.J. et al. (2007) Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol., 5, e310.
2. de la Bastide, M. and McCombie, W.R. (2007) Assembling genomic DNA sequences with PHRAP. Curr. Protoc. Bioinformatics, Chapter 11, Unit 11 14.
3. Ewing, B. and Green, P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res., 8, 186-194.
4. Excoffier, L. et al. (2005) Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evol. Bioinform. Online, 1, 47-50.
5. Filatov, D.A. (2002) PROSEQ: A software for preparation and evolutionary analysis of DNA sequence data sets.. Mol. Ecol. Notes, 2, 621-624.
6. Filatov, D.A. and Charlesworth, D. (1999) DNA polymorphism, haplotype structure and balancing selection in the Leavenworthia PgiC locus. Genetics, 153, 1423-1434.
7. Foxe, J.P. et al. (2008) Selection on amino acid substitutions in Arabidopsis. Mol. Biol. Evol., 25, 1375-1383.
8. Hein, J. et al. (2005) Gene Genealogies. Variation and Evolution. Oxford University Press, Oxford, UK.
9. Hey, J. and Nielsen, R. (2007) Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Natl Acad. Sci. USA, 104, 2785-2790.
10. Higgins, D.G. et al. (1996) Using CLUSTALfor multiple sequence alignments. Methods Enzymol., 266, 383-402.
11. Librado, P. and Rozas, J. (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
12. Nei, M. and Kumar, S. (2000) Molecular Evolution and Phylogenetics. Oxford University Press, New York.
13. Pritchard, J.K., Stephens, M. and Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
14. Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
15. Tamura, K. et al. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol., 24, 1596-1599.
16. Thornton, K. (2003) Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics, 19, 2325-2327.
17. Yang, Z. (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol., 24, 1586-1591.