Although in general the algorithm does not guarantee that the global minimum of the topological deviation is obtained, the constructed trees corresponding to local minima approximate the maximum topological similarity tree reasonably well. In cluster algorithm the notion of distance between groups of sequences is used for the setting of the branching order. This distance is defined as the arithmetic mean of pairwise distances between elements of the two groups. Contary to topological algorithm, in the cluster one the order of node connections is reconstituted together with the corresponding branch lengths. This property of cluster trees allows to introduce the distance from the root to each node and to draw the tree using this distance as a node abscissa.
All images have same size.
Width and height of the images may be set from 320 to 2000 and 240 to 1500 pixels, respectively. Defaults are 640 and 480. This option restrains the difference so that very short branches are plotted with length only at factor times less than maximum plotted. Such branches are dispayed in orange color. In the bootstrap a multiple alignment is resampled 100 times.