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Species Tree Estimation Using ASTRAL: Practical Considerations
Siavash Mirarab
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…
DiscoVista: interpretable visualizations of gene tree discordance
Erfan Sayyari, James B. Whitfield, Siavash Mirarab
Phylogenomics has ushered in an age of discordance. Analyses often reveal abundant discordances among phylogenies of different parts of genomes, as well as incongruences between sp…
Testing for polytomies in phylogenetic species trees using quartet frequencies
Erfan Sayyari, Siavash Mirarab
Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creatin…
Species tree estimation using ASTRAL: how many genes are enough?
Shubhanshu Shekhar, Sebastien Roch, Siavash Mirarab
Species tree reconstruction from genomic data is increasingly performed using methods that account for sources of gene tree discordance such as incomplete lineage sorting. One popu…