Methods in population genomics | Yann X.C. Bourgeois

There are many methods in population genomics. To help newcomers, we published a review on the main methods in the field, available here

This simple graph should explain it all…

A summary of an ideal popgen analytical pipeline

Methods are interconnected, and there is are more and more attempts to incorporate this connectivity in more recent works (e.g. machine learning). Aspects that require 'back-and-forth' are indicated by double arrows. Results obtained from methods listed in different sections can be used to inform the next steps of an analysis (single arrows). There is no one-size-fits-all pipeline, and elements of this general framework may be entirely omitted from an analysis depending on the research question

Table 1: Summary of methods dedicated to infer population structure.

	Software	Class of method	Purpose	Class of method	Issues/Warnings	Reference	Link

Table 2: Summary of methods dedicated to detect selection

	Software	Class of method	Purpose	Class of method	Issues/Warnings	Reference	Link

Table 3: Summary of methods dedicated to reconstruct demographic history

	Software	Class of method	Purpose	Class of method	Issues/Warnings	Reference	Link

Table 4: Summary of simulators and simulation-based methods for selection and demographic inference.

	Software	Class of method	Purpose	Class of method	Issues/Warnings	Reference	Link