Computational protocol: Effects of the HN Antigenic Difference between the Vaccine Strain and the Challenge Strain of Newcastle Disease Virus on Virus Shedding and Transmission

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Protocol publication

[…] Nucleotide sequence editing, analysis and prediction of amino acid sequences for the F and HN protein and alignments were conducted using the Clustal W multiple alignment method in the MegAlign 7.1.0 program of the Lasergene package (DNASTAR Inc., Madison, WI, USA). Phylogenetic trees based on the F and HN gene were both constructed by the program MEGA5 (Version 5.2), using the neighbor-joining method algorithm and the accession numbers of these NDVs were shown in the phylogenetic tree. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Human poliovirus 1 Mahoney
Diseases Newcastle Disease