Phylogenetic Analysis of ALV-J Associated with Immune Responses in Yellow Chicken Flocks in South China

Figure 5

Determination of reorganization events. (a) The PDR5 analyzed the recombination events of the virus isolates. The bootscan was based on the pairwise distance model, with a window size of 200, a step size of 50, and 1000 bootstrap replicates generated by the RDP5. (b) The SimPlot analysis graph of reorganized breakpoints. These were based on a 200-bp window; each step is 20 bp for comparison (100 self-expanding, setting a 90% consistent tree, neighbor-joining method, Kimura two-parameter model).

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