Computational protocol: Characterization of low pathogenicity avian influenza viruses isolated from wild birds in Mongolia 2005 through 2007

Similar protocols

Protocol publication

[…] Full genome sequencing of all isolates was performed as previously described []; Genbank accession numbers: GQ907286-GQ907357. Phylogenetic analysis was performed by aligning the nucleotide sequences of genes from the Mongolian viruses and selected reference isolates for the different lineages for each gene and aligning them with either ClustalV or ClustalW (Lasergene 7.1, DNASTAR, Madison, WI). Trees were constructed with merged duplicate runs of BEAST v. 1.4.8 [] using HKY substitution, empirical base frequency, Gamma heterogeneity, codon 2 partitions, relaxed lognormal clock, Yule Process tree prior with default operators with UPGMA starting tree and MCMC length of 107. […]

Pipeline specifications

Software tools Clustal W, BEAST
Application Phylogenetics
Organisms Anser indicus, Cygnus cygnus, Tadorna ferruginea, Chroicocephalus ridibundus, Netta rufina, Larus vegae
Diseases HIV Infections