AFLPDAT: a collection of R functions for convenient handling of AFLP data

被引：411

作者：

Ehrich, Dorothee ^{[1
]}

机构：

[1] Univ Oslo, Nat Hist Museum, Natl Ctr Biosystemat, NO-0318 Oslo, Norway

来源：

MOLECULAR ECOLOGY NOTES | 2006年 / 6卷 / 03期

关键词：

AFLP; data analysis software; input format conversion; phylogeography; population genetics; R;

D O I：

10.1111/j.1471-8286.2006.01380.x

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

AFLPDAT is a collection of R functions that facilitates the handling of dominant genotypic data. It converts data from a standard tab-separated table to the input formats of the following programs: ARLEQUIN, STRUCTURE, TREECON, PAUP and HICKORY. In addition, it calculates the proportion of polymorphic markers in each population, and estimates gene diversity as the average proportion of pairwise differences between individuals with confidence intervals based on bootstrapping across markers. It also produces summary tables of marker frequencies and the presence or absence of markers in each population. AFLPDAT can be downloaded from http://www.nhm.uio.no/ncb/.

引用

页码：603 / 604

页数：2

共 12 条

[1]

[Anonymous], 2001, PHYLOGENETIC ANAL US

[2]

Benham J.J., 2001, GENOGRAPHER

[3] Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study [J].

Evanno, G ;

Regnaut, S ;

Goudet, J .

MOLECULAR ECOLOGY, 2005, 14 (08) :2611-2620

[4] CONVERT: A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages [J].

Glaubitz, JC .

MOLECULAR ECOLOGY NOTES, 2004, 4 (02) :309-310

[5] A Bayesian approach to inferring population structure from dominant markers [J].

Holsinger, KE ;

Lewis, PO ;

Dey, DK .

MOLECULAR ECOLOGY, 2002, 11 (07) :1157-1164

[6] Nei's gene diversity and the index of average differences are identical measures of diversity within populations [J].

Kosman, E .

PLANT PATHOLOGY, 2003, 52 (05) :533-535

[7]

Net M., 1987, MOL EVOLUTIONARY GEN

[8]

Park S.D. E., 2001, Trypanotolerance in West African cattle and the population genetic effects of selection

[9]

Pritchard JK, 2000, GENETICS, V155, P945

[10]

R Development Core Team, 2004, R LANG ENV STAT COMP

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