Bookedited by François Pompanon and Aurélie Bonin.
Contents:
Sampling and experimental design: Sampling in landscape genomics / Stéphanie Manel, Cécile H. Albert, and Nigel G. Yoccoz. OligoTag : a program for designing sets of tags for next-generation sequencing of multiplexed samples / Eric Coissac. SNP discovery in non-model organisms using 454 next generation sequencing / Christopher W. Wheat. In silico fingerprinting (ISIF) : a user-friendly in silico AFLP program / Margot Paris and Laurence Després
Producing data: Diversity arrays technology : a generic genome profiling technology on open platforms / Andrzej Kilian [and others]. Two methods to easily obtain nucleotide sequences from AFLP loci of interest / Margot Paris [and others]. Roche genome sequencer flx based high-throughput sequencing of ancient DNA / David E. Alquezar-Planas and Sarah L. Fordyce. Preparation of normalized cDNA libraries for 454 titanium transcriptome sequencing / Zhao Lai [and others]. RAD paired-end sequencing for local de novo assembly and SNP discovery in non-model organisms / Paul D. Etter and Eric Johnson
Analyzing data: Automated scoring of AFLPs using RawGeno v 2.0, a free R CRAN library / Nils Arrigo, Rolf Holderegger, and Nadir Alvarez. Haplotype inference / Olivier Delaneau and Jean-François Zagury-- Allele identification in assembled genomic sequence datasets / Katrina M. Dlugosch and Aurélie Bonin. Multiple testing in large-scale genetic studies / Matthieu Bouaziz, MArine Jeanmougin, and Mickaël Guedj. Population genomic analysis of model and nonmodel organisms using sequenced RAD tags / Paul A. Hobenlobe, Julian Catchen, and William A. Cresko. Analysis and management of gene and allelic diversity in subdivided populations using the software program METAPOP / Andrés Pérez-Figueroa, Silvia T. Rodriquez-Ramillo, and ARmando Caballero. DetSel : an R-package to detect marker loci responding to selection / Renaud Vitalis. Use of qualitative environmental and phenotypic variables in the context of allele distribution models : detecting signatures of selection in the genome of Lake Victoria cichlids / Stéphane Joost [and others]. Genomic scan as a tool for assessing the genetic component of phenotypic variance in wild populations / Carlos M. Herrera.