Fabio Pardi

The paper presents algorithms for reconstructing past deletions in ancestral sequences using a deletion-only parsimony approach, providing exact solutions and graph-based representations of optimal reconstructions.

The paper introduces phylogenetic novelty scores to weight genetic sequences based on their evolutionary novelty, improving accuracy in character frequency estimation and other applications.

SHERPAS rapidly detects viral recombinants by analyzing phylogenetically-informed k-mers, outperforming existing methods in speed with minimal accuracy loss.

RAPPAS provides a fast, alignment-free method for phylogenetic placement of metagenomic sequences, achieving speed improvements over likelihood-based methods while maintaining accuracy.