How is the phylogenetic tree generated?
The phylogenetic tree, generated for the purpose of determining the identification of an isolate, is distance based. Accugenix uses the Neighbor Joining (NJ) Tree for data interpretation. The first step in generating a tree is a pairwise alignment of all of the sequences and calculation of the genetic distance for each pair. The resulting data is stored in a distance matrix. Using the data from the distance matrix, the algorithm then determines the tree topology that best represents the pairwise distances between all combinations. The distance along the horizontal lines connecting two organisms is a close approximation of the sequence differences between all pairs.
