Recently there has been increased use of statistical hypothesistesting in settings where the phylogenetic (evolutionary) relationshipamong organisms (taxa) should be considered. For example, we have acurrent need to assess our confidence in assigning influenza sequencesto the time period or species. We do so by using both: patternrecognition methods that do not explicitly account for the evolutionaryrelationships; and phylogenetic tree estimation methods that doexplicitly estimate the evolutionary relationships (branching order)among the specified taxa. We compare our conclusions under bothapproaches for sequences from the Hemagglutinin gene of the humaninfluenza RNA virus that are evenly distributed around the world from1985 to 1996 and for sequences of the Nucleoprotein gene of theinfluenza RNA virus from three host species
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