Download Vector NTI® Express Software User Guide

Guide Tree pane
Perform the
alignment
8
When you have selected the alignment settings, click on Submit.
Guide Tree pane
The Guide Tree, which resembles a Phylogenetic tree, is displayed when three or more sequences are aligned. The Guide Tree can be built using two different methods: • The Neighbor Joining method (NJ) of Saitou and Nei works on a matrix of distances between all pairs of sequence to be analyzed. These distances are related to the degree of divergence between the sequences.
• The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) is a simple agglomerative or hierarchical clustering method in which, at each step, the nearest two clusters are combined into a higher‐level cluster.
The Guide Tree is calculated after the sequences are aligned. AlignX displays the calculated distance values in parenthesis following the molecule name in the Guide Tree pane.
Graphs pane
The Graphs pane provides a graphical representation of sequence similarity and complexity among the aligned sequences.
The graphs in this pane interact with the sequences as listed in the Alignment pane.
Note: All graphs display the values averaged in a window of a specific length (defined by “window” parameter) that slides along the alignment.
Sequence
similarity graph
To generate the Similarity graph (upper graph), specific values (in a 0‐1 range) are assigned to each residue at a given alignment position in each aligned sequence, depending on whether the residue is identical, similar, or weakly similar to the corresponding residue of the consensus sequence. The values (1 (identical), 0.5 (similar), and 0.2 (weakly similar) for each residue at a given position are totaled; the sum is divided by the number of the sequences in the alignment, “normalizing” the resulting value.
Sequence
complexity graph
The Complexity graph (lower graph) is calculated as a sum of all pairwise residue substitution scores at a given alignment position divided by the number of pairs in the alignment. The scores are taken from the residue substitution matrix used for alignment calculation.
Vector NTI® Express Software User Guide
101