Automated scoring of AFLPs using RawGeno v 2.0, a Free R CRAN library

Methods in Molecular Biology

Volumn 888, Issue , 2012, Pages 155-175

  Arrigo, Nils ^a,b   Holderegger, Rolf ^c   Alvarez, Nadir ^b  

^a UNIVERSITY OF NEUCHÂTEL   (Switzerland)

^b UNIVERSITY OF LAUSANNE   (Switzerland)

^c SWISS FEDERAL RESEARCH INSTITUTE WSL   (Switzerland)

Author keywords

Bin editing; Command lines; Data mining; Graphical user interface; Scoring optimization

Indexed keywords

ALGORITHM; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; COMPUTER INTERFACE; FILTRATION; FLUORESCENCE ANALYSIS; GENE MAPPING; GENETIC MARKER; GENETIC VARIABILITY; GENOTYPE; HUMAN; MOLECULAR LIBRARY; PHYLOGEOGRAPHY; POPULATION GENETICS; PRIORITY JOURNAL; REPRODUCIBILITY; BIOLOGY; CHROMOSOME MAP; COMPUTER PROGRAM; DATA MINING; GENE LIBRARY; GENETIC POLYMORPHISM; GENETICS; METHODOLOGY; PLANT; PLANT GENOME;

ALGORITHMS; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DATA MINING; GENETIC MARKERS; GENOME, PLANT; GENOMIC LIBRARY; PLANTS; POLYMORPHISM, GENETIC; RESEARCH DESIGN; SOFTWARE;

EID: 84866750284     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-870-2_10     Document Type: Article

References (15)

1. Vos P, Hogers R, Bleeker M et al (1995) AFLP: a new technique for DNA fi ngerprinting. Nucleic Acids Res 23:4407-4414
2. Pompanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors: causes, consequences and solutions. Nat Rev Genet 6: 847-859
3. Meudt HM, Clarke AC (2007) Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci 12(3):106-117
4. Arrigo N, Tuszynski JW, Ehrich D, Gerdes T, Alvarez N (2009) Evaluating the impact of scoring parameters on the structure of intraspeci fi c genetic variation using RawGeno, an R package for automating AFLP scoring. BMC Bioinformatics. doi: 10.1186/1471-2105-10-33
5. Arrigo N, Felber F, Parisod C et al (2010) Origin and expansion of the allotetraploid Aegilops geniculata , a wild relative of wheat. New Phytol 187(4):1170-1180
6. Whitlock R, Hipperson H, Mannarelli M, Butlin RK, Burke T (2008) An objective, rapid and reproducible method for scoring AFLP peak-height data that minimizes genotyping error. Mol Ecol Resour 8:725-735
7. Herrmann D, Poncet BN, Manel S et al (2010) Selection criteria for scoring ampli fi ed fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates. Genome 53(4):302-310
8. Holland BR, Clarke AC, Meudt HM (2008) Optimizing automated AFLP scoring parameters to improve phylogenetic resolution. Syst Biol 57(3):347-366
9. Vekemans X, Beauwens T, Lemaire M, Roldan-Ruiz I (2002) Data from ampli fi ed fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Mol Ecol 11(1):139-151
10. Paris M, Bonnes B, Ficetola GF, Poncet BN, Després L (2010) Ampli fi ed fragment length homoplasy: in silico analysis for model and non-model species. BMC Genomics. doi: 10.1186/1471-2164-11-287
11. Ehrich D (2006) AFLPdat: a collection of R functions for convenient handling of AFLP data. Mol Ecol Notes 6:603-604
12. Gort G, van Eeuwijk F (2010) Codominant scoring of AFLP in association panels. Theor Appl Genet. doi: 10.1007/s00122-010-1313-x
13. Bonin A, Bellemain E, Eidesen PB et al (2004) How to track and assess genotyping errors in population genetics studies. Mol Ecol 13:3261-3273
14. Gugerli F, Englisch T, Niklfeld H et al (2008) Relationships among levels of biodiversity and the relevance of intraspeci fi c diversity in conservation- A project synopsis. Perspect Plant Ecol Evol Systemat 10:259-281
15. Peintiger M, Arrigo N, Brodbeck S et al (2010) Genetische und morphologische Differenzierung der endemischen Grasart Deschampsia littoralis (Gaudin) Reut.-Wie verschieden sind die Population am Bodensee und am Lac de Joux im Vergleich zu D. cespitosa (L.) P. Beauv. Vogelwarte Radolfszell, University of Neuchâtel, WSL