id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-017354-cndb031c	Janies, D.	Large-Scale Phylogenetic Analysis of Emerging Infectious Diseases	2008		.txt	text/plain	12429	648	45	The products of a phylogenetic analysis are a graphical tree of ancestor-descendent relationships and an inferred summary of mutations, recombination events, host shifts, geographic, and temporal spread of the viruses. Given a tree and a data matrix of sequences and features, the parsimony method can pinpoint the branches on which certain evolutionary events are inferred to occur between ancestor or descendent. Phylogenetic analysis of large genomic datasets can present several nested NPcomplete problems: multiple alignment, tree-search, and in some cases, gene order and complement differences among organisms. We provide exemplar cases in which phylogenetic analyses of viral genomes have been crucial to understand complex patterns of transmission among animal and human hosts: Severe Acute Respiratory Syndrome (SARS) [KSI03] and influenza [WEB92] . Molecular phylogenetic analyses of the nucleotide or inferred amino acid sequence data from various viral isolates can then be used to reconstruct the history of the transmission events the virus among hosts.	./cache/cord-017354-cndb031c.txt	./txt/cord-017354-cndb031c.txt