Selected article for: "maximum likelihood method and phylogenetic analysis"
Author: Li, Ji Lian; Cornman, R. Scott; Evans, Jay D.; Pettis, Jeffery S.; Zhao, Yan; Murphy, Charles; Peng, Wen Jun; Wu, Jie; Hamilton, Michele; Boncristiani, Humberto F.; Zhou, Liang; Hammond, John; Chen, Yan Ping
Title: Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera
  • Document date: 2014_1_21
    • ID: wxiazglk_36
    Snippet: Phylogenetic analysis. The sequences of the 731-bp TRSV fragment amplified from the region encoding the capsid protein by the primer pair TRSV-F2 and TRSV-R2 from honeybees, bee pollen, and Varroa mites were compared with existing GenBank sequences isolated from plants. Phylogenetic analysis was conducted in MEGA4 (63) . The sequences were aligned using ClustalW, and the sequences that could not be aligned unambiguously at both 3= and 5= ends wer.....
    Document: Phylogenetic analysis. The sequences of the 731-bp TRSV fragment amplified from the region encoding the capsid protein by the primer pair TRSV-F2 and TRSV-R2 from honeybees, bee pollen, and Varroa mites were compared with existing GenBank sequences isolated from plants. Phylogenetic analysis was conducted in MEGA4 (63) . The sequences were aligned using ClustalW, and the sequences that could not be aligned unambiguously at both 3= and 5= ends were truncated. A tree was built using the neighbor-joining method (64) with distances computed using the maximum composite likelihood method (65) . The reliability of the phylogenies was assessed by bootstrap replication (500 replicates) (66) . Node labels correspond to bootstrap support, and values of Ͼ50% were regarded as evidence for the phylogenetic grouping.

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