Chao Zhang

The paper introduces D+ and D* statistics to improve detection of gene flow by addressing saturation bias in deeper phylogenies using multiallelic site patterns.

WASTER infers shallow phylogenies from low-coverage short reads without assembly or alignment, achieving accuracy comparable to traditional methods at lower costs.

This paper introduces CASTLES-Pro, a method for estimating species tree branch lengths that accounts for gene duplication, loss, and incomplete lineage sorting, showing improved accuracy over existing methods.

TAPER identifies and removes small stretches of error in sequence alignments while preserving most of the data, improving alignment accuracy.

ASTRAL-Pro improves species tree inference by handling gene duplication and loss, outperforming existing methods in complex scenarios.

AmpliconReconstructor integrates optical mapping and NGS to resolve focal amplifications in cancer, revealing complex structures and origins of ecDNA and other rearrangements.