Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding

被引：410

作者：

Brown, Samuel D. J. ^{[1
]}

Collins, Rupert A. ^{[1
]}

Boyer, Stephane ^{[2
]}

Lefort, Marie-Caroline ^{[1
]}

Malumbres-Olarte, Jagoba ^{[2
]}

Vink, Cor J. ^{[3
,4
]}

Cruickshank, Robert H. ^{[2
]}

机构：

[1] Lincoln Univ, Bioprotect Res Ctr, Canterbury 7647, New Zealand

[2] Lincoln Univ, Dept Ecol, Fac Agr & Life Sci, Canterbury 7647, New Zealand

[3] AgResearch, Biosecur Grp, Christchurch 8140, New Zealand

[4] Lincoln Univ, Entomol Res Museum, Lincoln 7647, New Zealand

来源：

MOLECULAR ECOLOGY RESOURCES | 2012年 / 12卷 / 03期

关键词：

barcoding gap; characteristic attributes; integrative taxonomy; mini-barcodes; neighbour-joining; threshold optimization;

D O I：

10.1111/j.1755-0998.2011.03108.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：

Spider: SPecies IDentity and Evolution in R is a new R package implementing a number of useful analyses for DNA barcoding studies and associated research into species delimitation and speciation. Included are functions essential for generating important summary statistics from DNA barcode data, assessing specimen identification efficacy, and for testing and optimizing divergence threshold limits. In terms of investigating evolutionary and taxonomic questions, techniques for assessing diagnostic nucleotides and probability of reciprocal monophyly are also provided. Additionally, a sliding window function offers opportunities to analyse information across a gene, essential for marker design in degraded DNA studies. Spider capitalizes on Rs extensible ethos and offers an integrated platform ideal for the analysis of both nucleotide and morphological data. The program can be obtained from the comprehensive R archive network (CRAN, ) and from the R-Forge package development site ().

引用

页码：562 / 565

页数：4

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