Analysis of Amino Acid Changes in the Fusion Protein of Virulent Newcastle Disease Virus from Vaccinated Poultry in Nigerian Isolates

Figure 3

Molecular phylogenetic analysis based on the nucleotide sequences of the F-gene of study isolates, some reported NDV isolates and known vaccine strains using bootstrap consensus of 1000 replicates. The evolutionary history was inferred by using the Maximum Likelihood method and JTT matrix-based model [15]. The tree with the highest log likelihood (–20685.06) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the JTT model, and then selecting the topology with superior log likelihood value. This analysis involved 61 amino acid sequences. There were a total of 1662 positions in the final dataset. Evolutionary analyses were conducted in MEGA11 [16].