S. Mirarab

CASTER: Direct species tree inference from whole-genome alignments

CASTER infers species trees directly from whole-genome alignments by addressing discordance without predefining recombination-free loci, showing scalability and accuracy in simulations and real data.

Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees

This paper introduces weighting schemes for quartet-based species tree inference to improve accuracy by reducing the impact of noisy gene trees, outperforming existing methods in simulations and empirical data.

Scalable Models of Antibody Evolution and Benchmarking of Clonal Tree Reconstruction Methods

This paper benchmarks clonal tree reconstruction methods using a scalable model of antibody evolution and finds that simple postprocessing improves accuracy over alternative methods.

Gene exchange networks define species-like units in marine prokaryotes

The paper identifies gene exchange networks in marine prokaryotes, showing they form broader evolutionary units than traditional species definitions.

Assembly-free and alignment-free sample identification using genome skims

The paper introduces Skmer, an alignment-free tool that uses k-mer decomposition to estimate genomic distances from genome skims, achieving high accuracy in identifying closest matches and inferring phylogeny.

Fine-mapping the Favored Mutation in a Positive Selective Sweep

This paper introduces iSAFE, a method to identify the favored mutation in selective sweeps, and demonstrates its effectiveness on simulated and human genomic data.