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1. Next-generation sequencing (NGS) techniques have facilitated the production of an ever-increasing number of genetic markers across genomes of non-model species, allowing for the study of variation in these markers across natural populations to deepen understanding of how population history and selection act on genomes.

2. Population genomics now provides tools to better integrate selection into a historical framework and take into account selection when reconstructing demographic history, but the burst of analytical tools can confuse users and limit effective information retrieval from complex genomic datasets.

3. To address this need, the article describes possible analytical protocols and links them with more than 70 methods dealing with genome-scale datasets, summarizing their strategies to infer demographic history and selection while discussing some limitations. A website listing these methods is available at www.methodspopgen.com.

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