Computational protocol: A(H1N1)pdm09 influenza infection: vaccine inefficiency

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Protocol publication

[…] For the phylogenetic analysis, Influenza Hemagglutinin gene-specific primers were used [, ]. The Sequencher® 5.0 program (Gencodes Corporation, Ann Arbor, MI) was used to compare the nucleotide sequences of the collected samples to HA genes of various Influenza A clades.The evolutionary relationships and the most recent common ancestor (MRCA) for the influenza A(H1N1)pdm09 virus Hemagglutinin sequences, were calculated using a Bayesian Markov chain Monte Carlo (MCMC) method, applied using a relaxed molecular clock, as implemented in the BEAST program (version 1.7.5). Trees were visualized and edited with the Figure Tree program (version 1.4.2) included in the BEAST software package []. […]

Pipeline specifications

Software tools Sequencher, BEAST
Application Phylogenetics
Organisms Sus scrofa
Diseases Influenza, Human
Chemicals Amino Acids