Bioinformatics Vol. 19 no. 18 2003
pages 2496-2497
© 2003 Oxford University Press
Applications Note |
DnaSP, DNA polymorphism analyses by the coalescent and other methods
1 Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Diagonal 645, 08071 Barcelona, Spain and 2 Departament de Llenguatges i Sistemes Informàtics, Universitat Politècnica de Catalunya, Barcelona, Spain
Received on February 28, 2003
; revised on June 6, 2003
; accepted on July 8, 2003
Summary: DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (
5 Mb per sequence); (2) conducting a large number of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical outputs for an easy visualization of results.
Availability: The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp
Contact: jrozas{at}ub.edu
* To whom correspondence should be addressed.
Present address: Departament de Tecnología, Universitat Pompeu Fabra, Barcelona, Spain.
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R. S. Baucom, J. C. Estill, J. Leebens-Mack, and J. L. Bennetzen Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome Genome Res., February 1, 2009; 19(2): 243 - 254. [Abstract] [Full Text] [PDF]
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D. Alvarez-Ponce, M. Aguade, and J. Rozas Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes Genome Res., February 1, 2009; 19(2): 234 - 242. [Abstract] [Full Text] [PDF]
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M. Carneiro, N. Ferrand, and M. W. Nachman Recombination and Speciation: Loci Near Centromeres Are More Differentiated Than Loci Near Telomeres Between Subspecies of the European Rabbit (Oryctolagus cuniculus) Genetics, February 1, 2009; 181(2): 593 - 606. [Abstract] [Full Text] [PDF]
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P. Touzet and L. F. Delph The Effect of Breeding System on Polymorphism in Mitochondrial Genes of Silene Genetics, February 1, 2009; 181(2): 631 - 644. [Abstract] [Full Text] [PDF]
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C. N. Balakrishnan and S. V. Edwards Nucleotide Variation, Linkage Disequilibrium and Founder-Facilitated Speciation in Wild Populations of the Zebra Finch (Taeniopygia guttata) Genetics, February 1, 2009; 181(2): 645 - 660. [Abstract] [Full Text] [PDF]
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K. S. Caldwell and R. W. Michelmore Arabidopsis thaliana Genes Encoding Defense Signaling and Recognition Proteins Exhibit Contrasting Evolutionary Dynamics Genetics, February 1, 2009; 181(2): 671 - 684. [Abstract] [Full Text] [PDF]
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K. J. Balbi, E. P.C. Rocha, and E. J. Feil The Temporal Dynamics of Slightly Deleterious Mutations in Escherichia coli and Shigella spp. Mol. Biol. Evol., February 1, 2009; 26(2): 345 - 355. [Abstract] [Full Text] [PDF]
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J. H. Hur, K. Van Doninck, M. L. Mandigo, and M. Meselson Degenerate Tetraploidy Was Established Before Bdelloid Rotifer Families Diverged Mol. Biol. Evol., February 1, 2009; 26(2): 375 - 383. [Abstract] [Full Text] [PDF]
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M. Wu, J. M. Comeron, H. S. Yoon, and D. Bhattacharya Unexpected Dynamic Gene Family Evolution in Algal Actins Mol. Biol. Evol., February 1, 2009; 26(2): 249 - 253. [Abstract] [Full Text] [PDF]
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R. Reina, E. Grego, L. Bertolotti, D. De Meneghi, and S. Rosati Genome Analysis of Small-Ruminant Lentivirus Genotype E: a Caprine Lentivirus with Natural Deletions of the dUTPase Subunit, vpr-Like Accessory Gene, and 70-Base-Pair Repeat of the U3 Region J. Virol., January 15, 2009; 83(2): 1152 - 1155. [Abstract] [Full Text] [PDF]
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E. Vanlaere, A. Baldwin, D. Gevers, D. Henry, E. De Brandt, J. J. LiPuma, E. Mahenthiralingam, D. P. Speert, C. Dowson, and P. Vandamme Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov. Int J Syst Evol Microbiol, January 1, 2009; 59(1): 102 - 111. [Abstract] [Full Text] [PDF]
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 M. Andrew, T.L. Peever, and B.M. Pryor An expanded multilocus phylogeny does not resolve morphological species within the small-spored Altemrnaria species complex. Mycologia, January 1, 2009; 101(1): 95 - 109. [Abstract] [Full Text] [PDF]
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H. Chen, P. L. Morrell, V. E. T. M. Ashworth, M. de la Cruz, and M. T. Clegg Tracing the Geographic Origins of Major Avocado Cultivars J. Hered., January 1, 2009; 100(1): 56 - 65. [Abstract] [Full Text] [PDF]
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F. Rodriguez, S. Hammer, T. Perez, F. Suchentrunk, R. Lorenzini, J. Michallet, N. Martinkova, J. Albornoz, and A. Dominguez Cytochrome b Phylogeography of Chamois (Rupicapra spp.). Population Contractions, Expansions and Hybridizations Governed the Diversification of the Genus J. Hered., January 1, 2009; 100(1): 47 - 55. [Abstract] [Full Text] [PDF]
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S. E. Alter, S. F. Ramirez, S. Nigenda, J. U. Ramirez, L. R. Bracho, and S. R. Palumbi Mitochondrial and Nuclear Genetic Variation across Calving Lagoons in Eastern North Pacific Gray Whales (Eschrichtius robustus) J. Hered., January 1, 2009; 100(1): 34 - 46. [Abstract] [Full Text] [PDF]
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J. A. Anderson, W. D. Gilliland, and C. H. Langley Molecular Population Genetics and Evolution of Drosophila Meiosis Genes Genetics, January 1, 2009; 181(1): 177 - 185. [Abstract] [Full Text] [PDF]
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M. Aguade Nucleotide and Copy-Number Polymorphism at the Odorant Receptor Genes Or22a and Or22b in Drosophila melanogaster Mol. Biol. Evol., January 1, 2009; 26(1): 61 - 70. [Abstract] [Full Text] [PDF]
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A. N. Lau, L. Peng, H. Goto, L. Chemnick, O. A. Ryder, and K. D. Makova Horse Domestication and Conservation Genetics of Przewalski's Horse Inferred from Sex Chromosomal and Autosomal Sequences Mol. Biol. Evol., January 1, 2009; 26(1): 199 - 208. [Abstract] [Full Text] [PDF]
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 T. B. Wells, G. Zhang, Z. Harley, and H. Vaziri Genetic Hypervariability in Two Distinct Deuterostome Telomerase Reverse Transcriptase Genes and their Early Embryonic Functions Mol. Biol. Cell, January 1, 2009; 20(1): 464 - 480. [Abstract] [Full Text] [PDF]
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K. Kurata, T. Jaffre, and H. Setoguchi Genetic diversity and geographical structure of the pitcher plant Nepenthes vieillardii in New Caledonia: A chloroplast DNA haplotype analysis Am. J. Botany, December 1, 2008; 95(12): 1632 - 1644. [Abstract] [Full Text] [PDF]
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C. R. Linnen and B. D. Farrell Comparison of Methods for Species-Tree Inference in the Sawfly Genus Neodiprion (Hymenoptera: Diprionidae) Syst Biol, December 1, 2008; 57(6): 876 - 890. [Abstract] [Full Text] [PDF]
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