Bioedit degap
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There are a number of programs for inferring phylogenies including, but not limited to, PAUP*, BAMBE, BEAST, PHYLIP RAxML and MrBayes. Broadly speaking, phylogenetics is the study of evolutionary relationships among organisms or taxon. Īlthough there are a number of programs available for clustering nucleotide sequences (e.g., BLASTClust, UPGMA and WPGMA, neighbor-joining (NJ), and phyclust ), phylogenetic approaches have been ubiquitous in the literature involving HIV-1 transmission clusters. In other studies performed outside of Quebec, phylogenetic clusters have been used to provide crucial insights about the spread and transmission of the disease. Previous population-based studies involving the phylogenetic analysis of Quebec’s primary HIV infection cohort have revealed clusters that correlate with distinct social networks and risk behaviours. This percentage is second only to the province of Ontario, which contributed 39.6 % of the total HIV cases in the PHAC report. Of the 2090 reported HIV cases in 2013, Quebec accounted for 21.7 %. In a 2013 surveillance report released by the Public Health Agency of Canada (PHAC), it is estimated that a cumulative total of 78,511 cases of HIV have been reported in Canada since 1985. The present paper aims at developing new techniques for identifying clusters of genetically similar DNA sequences and pays particular attention to HIV-infected individuals from Quebec, Canada. This endeavour is particularly important in genetics where the sheer volume of data renders many popular clustering techniques prohibitive or ineffective. In an age overwhelmed by a massive influx of data, the need for fast and effective clustering techniques has never been greater.