Computer programs for population genetics data analysis: a survival guide

被引：253

作者：

Excoffier, Laurent ^{[1
]}

Heckel, Gerald ^{[1
]}

机构：

[1] Univ Bern, Inst Zool, CMPG, CH-3012 Bern, Switzerland

来源：

NATURE REVIEWS GENETICS | 2006年 / 7卷 / 10期

关键词：

D O I：

10.1038/nrg1904

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

The analysis of genetic diversity within species is vital for understanding evolutionary processes at the population level and at the genomic level. A large quantity of data can now be produced at an unprecedented rate, requiring the use of dedicated computer programs to extract all embedded information. Several statistical packages have been recently developed, which offer a panel of standard and more sophisticated analyses. We describe here the functionalities, special features and assumptions of more than 20 such programs, indicate how they can interoperate, and discuss new directions that could lead to improved software and analyses.

引用

页码：745 / 758

页数：14

共 65 条

[1] Population history and natural selection shape patterns of genetic variation in 132 genes [J].

Akey, JM ;

Eberle, MA ;

Rieder, MJ ;

Carlson, CS ;

Shriver, MD ;

Nickerson, DA ;

Kruglyak, L .

PLOS BIOLOGY, 2004, 2 (10) :1591-1599

[2] A haplotype map of the human genome [J].

Altshuler, D ;

Brooks, LD ;

Chakravarti, A ;

Collins, FS ;

Daly, MJ ;

Donnelly, P ;

Gibbs, RA ;

Belmont, JW ;

Boudreau, A ;

Leal, SM ;

Hardenbol, P ;

Pasternak, S ;

Wheeler, DA ;

Willis, TD ;

Yu, FL ;

Yang, HM ;

Zeng, CQ ;

Gao, Y ;

Hu, HR ;

Hu, WT ;

Li, CH ;

Lin, W ;

Liu, SQ ;

Pan, H ;

Tang, XL ;

Wang, J ;

Wang, W ;

Yu, J ;

Zhang, B ;

Zhang, QR ;

Zhao, HB ;

Zhao, H ;

Zhou, J ;

Gabriel, SB ;

Barry, R ;

Blumenstiel, B ;

Camargo, A ;

Defelice, M ;

Faggart, M ;

Goyette, M ;

Gupta, S ;

Moore, J ;

Nguyen, H ;

Onofrio, RC ;

Parkin, M ;

Roy, J ;

Stahl, E ;

Winchester, E ;

Ziaugra, L ;

Shen, Y .

NATURE, 2005, 437 (7063) :1299-1320

[3]

Anderson EC, 2002, GENETICS, V160, P1217

[4]

Balloux F, 2000, EVOLUTION, V54, P1414, DOI 10.1111/j.0014-3820.2000.tb00573.x

[5]

Beaumont MA, 1999, GENETICS, V153, P2013

[6] The Bayesian revolution in genetics [J].

Beaumont, MA ;

Rannala, B .

NATURE REVIEWS GENETICS, 2004, 5 (04) :251-261

[7]

Beaumont MA, 2002, GENETICS, V162, P2025

[8] Identifying adaptive genetic divergence among populations from genome scans [J].

Beaumont, MA ;

Balding, DJ .

MOLECULAR ECOLOGY, 2004, 13 (04) :969-980

[9] Evaluating loci for use in the genetic analysis of population structure [J].

Beaumont, MA ;

Nichols, RA .

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 1996, 263 (1377) :1619-1626

[10] Comparison of Bayesian and maximum-likelihood inference of population genetic parameters [J].

Beerli, P .

BIOINFORMATICS, 2006, 22 (03) :341-345

← 1 2 3 4 5 6 7 →