Louis Ranjard

AFPhyloMix reconstructs haplotype phylogenies from pooled short-read sequences without barcoding, achieving 80% accuracy for up to 15 haplotypes in simulations and real data.

This paper introduces a dynamic programming algorithm for improving DNA sequence assembly with very low coverage by updating the reference sequence dynamically, achieving better alignment and assembly quality.

HaploJuice improves haplotype assembly accuracy by estimating sub-sample proportions and using dynamic programming, outperforming existing methods on simulated and real data.