Species Tree Estimation Using ASTRAL: Practical Considerations

TL;DR

This paper discusses practical aspects of using ASTRAL for species tree estimation, including input preparation, output interpretation, and analysis follow-up, highlighting its strengths and limitations in phylogenomic studies.

Contribution

It provides a comprehensive review of practical considerations and best practices for applying ASTRAL in species tree reconstruction.

Findings

ASTRAL is statistically consistent under the multi-species coalescent model.

It is scalable and highly accurate in simulated and empirical studies.

Practical guidelines improve the reliability of species tree estimation using ASTRAL.

Abstract

ASTRAL is a method for reconstructing species trees after inferring a set of gene trees and is increasingly used in phylogenomic analyses. It is statistically consistent under the multi-species coalescent model, is scalable, and has shown high accuracy in simulated and empirical studies. This chapter discusses practical considerations in using ASTRAL, starting with a review of published results and pointing to the strengths and weaknesses of species tree estimation using ASTRAL. It then continues to detail the best ways to prepare input gene trees, interpret ASTRAL outputs, and perform follow-up analyses.