Computational protocol: Characterization of the Influenza A H5N1 Viruses of the 2008-09 Outbreaks in India Reveals a Third Introduction and Possible Endemicity

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Protocol publication

[…] Representative sequences of the H5N1 viruses belonging to the Z genotype were selected from the GenBank based on sequence identity (100% identical sequences were excluded) and including wherever possible isolates whose whole genomes were available. Multiple nucleotide and amino acid sequence alignments for all eight gene segments were performed using Clustalx version 1.83 . Phylogenetic analysis was performed using the neighbour-joining method with the Kimura 2-parameter distance model and 1000 bootstrap replicates using MEGA version 4 . The percent nucleotide identity (PNI) and percent amino acid identity (PAI) values were calculated as pairwise p-distances. The tree topologies were confirmed by using the Bayesian approach for tree construction as implemented in Mr Bayes 3.2 . The GTR (General Time Reversible)+I (Invariable sites) model with gamma-distributed rate variation across sites and a proportion of invariable sites, was specifically used and other parameters were kept as default. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Homo sapiens
Diseases Infection