Computational protocol: Characterisation of a highly pathogenic influenza A virus of subtype H5N2 isolated from ostriches in South Africa in 2004

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Protocol publication

[…] Reverse‐transcriptase‐polymerase‐chain reaction products were sequenced by cycle‐sequencing reactions using ABI Terminator cycle sequencing V1·1 chemistry on a Perkin‐Elmer ABI PrismTM 310 DNA sequencer (Applied Biosystems, Foster City, USA). Sequence data was assembled and edited using the Lasergene version 7 seqman software (DNASTAR Inc.). Sequence alignments were performed using the Lasergene version 7 megalign software (DNASTAR Inc). Maximum Likelihood trees were generated using Phylogeny Inference Package (phylip) software version 3·57c with the transition to transversion ratio for the data set calculated using tree‐puzzle v5·2. Nucleotide distance matrices were generated using the Lasergene version 7 megalign software (DNASTAR Inc). For phylogenetic tree construction and comparison, sequences generated from isolates submitted to VLA Weybridge as part of its EU/OIE/FAO Reference Laboratory status or obtained from the Influenza Sequence Database (ISD), Los Alamos, USA were included in the trees. Sequences submitted to GenBank were assigned the accession numbers FJ519978–FJ519989. […]

Pipeline specifications

Software tools PHYLIP, TREE-PUZZLE
Application Phylogenetics
Organisms Influenza A virus, Struthio camelus, Gallus gallus, Anas platyrhynchos
Diseases Influenza, Human