Arlequin (version 3.0): An integrated software package for population genetics data analysis

Evolutionary Bioinformatics - Tập 1 - Trang 117693430500100 - 2005
Laurent Excoffier1, Guillaume Laval1, Stefan Schneider1
1Computational and Molecular Population Genetics Lab, Zoological Institute, University of Berne, Baltzerstrasse 6, 3012 Berne, Switzerland

Tóm tắt

Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3 .

Từ khóa


Tài liệu tham khảo

10.1186/1471-2156-5-22

Chakraborty R., 1990, Am J Hum Genet., 47, 87

10.1046/j.1471-8286.2003.00582.x

Excoffier L., 2003, Handbook of Statistical Genetics, 2, 713

10.1046/j.1365-294X.2003.02004.x

Excoffier L., 2003, Mol Ecol., 1, 7

Excoffier L., 1995, Mol Biol Evol., 12, 921

Excoffier L., 1992, Genetics., 131, 479, 10.1093/genetics/131.2.479

Fu Y-X., 1997, Genetics., 147, 915, 10.1093/genetics/147.2.915

10.1098/rspb.2000.0970

10.1093/oxfordjournals.jhered.a111627

Goudet J., 1996, Genetics., 144, 1933, 10.1093/genetics/144.4.1933

10.2307/2532296

Hedrick P., 1987, Genetics., 117, 331, 10.1093/genetics/117.2.331

Hudson R.R., 1990, Oxford Surveys in Evolutionary Biology., 1

10.2135/cropsci2000.4061521x

10.1093/bioinformatics/bth264

10.1016/S0169-5347(99)01632-8

Nordborg M., 2003, Handbook of Statistical Genetics, 2nd edition., 602

Paetkau D., 1997, Genetics., 147, 1943, 10.1093/genetics/147.4.1943

10.1093/molbev/msg009

10.2307/2410454

10.1093/oxfordjournals.jhered.a111573

Reynolds J., 1983, Genetics., 105, 767, 10.1093/genetics/105.3.767

Rogers A.R., 1992, Mol Biol Evol., 9, 552

10.1093/bioinformatics/btg359

Schnabel A., 1998, Advances in Molecular Ecology., 291

Schneider S., 1999, Genetics., 152, 1079, 10.1093/genetics/152.3.1079

Schneider S., 2000, Arlequin: a software for population genetics data analysis.

Slatkin M., 1995, Genetics., 139, 457, 10.1093/genetics/139.1.457

10.1017/S0016672300034236

10.1038/hdy.1996.55

10.2307/2413122

Tajima F., 1989, Genetics., 123, 585, 10.1093/genetics/123.3.585

Watterson G., 1978, Genetics., 88, 405, 10.1093/genetics/88.2.405

Weir B.S., 1996, Genetic Data Analysis II: Methods for Discrete Population Genetic Data.

Thông tin
Thông tin xuất bản

Evolutionary Bioinformatics

Tập 1

117693430500100

Thông tin tác giả