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The Three Mosquitos The short story about the phylogenetic group Define the molecular epidemiology of HBV in Tunisia • • • • Samples from blood donors Full genome sequences Phylogenetic analyses Check for eventual new subtypes? Workflow DNA sequences ENA database PAUP Alignment CLUSTAL Omega AliView Phylogenetic analysis Evolution model JModeltest Maximum likelihood RAxML Bayesian Mr Bayes Neighbour Joining (NJ) CLUSTAL Omega Phylogenetic Trees FigTree Recombination Simplot ML tree Recombination analysis Conclusions • Workflow for phylogenetic analysis • New programs and resources • ENA, PAUP, AliView, JModeltest, RAxML, Mr Bayes, FigTree, Simplot • New things we have learned • Unix commands • Keep file names short but descriptive • No spaces in file names Recommendations • Back-up • Keep track of your work • Keep proper file format • Check the manual first • Ask the experts • ‘slack them’ Acknowledgments Birgit Meldal Pinky Langat
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