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Since its emergence in March 2009, the pandemic 2009 H1N1 influenza A virus has posed a serious threat to public health. To trace the evolutionary path of these new pathogens, we performed a selection-pressure analysis of a large number of hemagglutinin (HA) and neuraminidase (NA) gene sequences of H1N1 influenza viruses from different hosts. Phylogenetic(More)
Explicit evolutionary models are required in maximum-likelihood and Bayesian inference, the two methods that are overwhelmingly used in phylogenetic studies of DNA sequence data. Appropriate selection of nucleotide substitution models is important because the use of incorrect models can mislead phylogenetic inference. To better understand the performance of(More)
A well-informed choice of genetic locus is central to the efficacy of DNA barcoding. Current DNA barcoding in animals involves the use of the 5' half of the mitochondrial cytochrome oxidase 1 gene (CO1) to diagnose and delimit species. However, there is no compelling a priori reason for the exclusive focus on this region, and it has been shown that it(More)
For some groups of organisms, DNA barcoding can provide a useful tool in taxonomy, evolutionary biology, and biodiversity assessment. However, the efficacy of DNA barcoding depends on the degree of sampling per species, because a large enough sample size is needed to provide a reliable estimate of genetic polymorphism and for delimiting species. We used a(More)
Phylogenetic analysis has achieved extraordinary results in domains like species delimitation and evolutionary biology. An essential element behind this success has been the introduction of high performance computing techniques in the step of estimating the phylogenetic likelihoods. This paper describes the design and implementation of a distributed and(More)
Searching for the evolutionary relationships between groups of organism has become a routine procedure in molecular biology. MrBayes is a popular model based phylogenetic inference tool using Bayesian statistics. Unfortunately, the computational cost is very high, resulting in undesirably long execution time. In this paper, we present what we believe the(More)
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