id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-000463-31q7ftnd	Jombart, T	Reconstructing disease outbreaks from genetic data: a graph approach	2010-06-16		.txt	text/plain	5094	251	45	Within this framework, we developed an algorithm called SeqTrack, which directly reconstructs the most plausible genealogy of a set of sampled isolates, allowing for a direct assessment of the spatiotemporal dynamics of the epidemic under study. SeqTrack algorithm Our method aims to reconstruct the transmission tree of pathogens during a disease outbreak, using genotypes and collection dates to uncover ancestries between sampled isolates. Given the low levels of genetic diversity expected during the early stages of disease outbreaks, isolates with identical haplotypes but different collection dates and Figure 1 Illustration of possible reconstructions of genealogical relations. Having tested the ability of the method at reconstructing transmission trees from outbreak genetic data, we used SeqTrack to infer the spatiotemporal dynamics of the early stage of the 2009 swine-origin A/H1N1 influenza pandemic. Using simulated data, we showed the originality of this method compared to classical phylogenetic reconstruction, and its ability to infer correct genealogies of isolates in densely sampled disease outbreaks.	./cache/cord-000463-31q7ftnd.txt	./txt/cord-000463-31q7ftnd.txt