Chao Zhang

Beyond infinite sites: Generalized ABBA-BABA statistic for deeper phylogenies

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: Practical de novo phylogenomics from low-coverage short reads

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

Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss

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: Pinpointing errors in multiple sequence alignments despite varying rates of evolution

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

ASTRAL-Pro: quartet-based species tree inference despite paralogy

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

AmpliconReconstructor: Integrated analysis of NGS and optical mapping resolves the complex structures of focal amplifications in cancer

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