Computational protocol: Phylogenetic analysis of Chinese sheeppox and goatpox virus isolates

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Protocol publication

[…] The nucleotide sequences of P32 gene, GPCR gene and RPO30 gene of other capripoxvirus strains were obtained from the GenBank database using online BLAST program on NCBI. Multiple-alignment of these sequences was performed by MEGA 4 (version 4.0) with ClustalW method. Then, MEGA 4 was used to perform phylogenetic analysis with Neighbor-Joining (NJ), Maximum Parsimony (MP) and Minimum Evolution (ME) [,]. Reliability of phylogenetic trees was tested by bootstrap analysis with 1000 replicates []. All the methods resulted in similar topological trees. The consensus MP trees were reconstructed and shown as rectangular trees in Figure , , . For further confirmation, three other phylogenetic trees were reconstructed using Phylip v3.69. In brief, the sequences were aligned by ClustalW2 []. The phylogenetic trees were reconstructed with MP method, calculated using the modules SEQBOOT, DNAPARS and CONSENSE of Phylip v3.69 package. The phylogenetic trees were displayed by Tree-View program []. […]

Pipeline specifications

Software tools MEGA, Clustal W, PHYLIP
Application Phylogenetics
Organisms Ovis aries, Capra hircus, Sheeppox virus
Diseases HIV Infections