We work on creation of user interfaces to facilitate different types of protein structure-function analyses. Shown below is one of our user interfaces, the PhyloScope viewer for phylogenetic trees, written in JavaScript. PhyloScope supports coloring and collapsing of subtrees, selection of subsets of leaves, and linking of leaf icons to internet resources. PhyloScope is available for viewing phylogenetic trees in the PhyloFacts resource. We highlight on the tree which sequences are in SwissProt, which have experimental support for their annotations, and which are discussed in the literature. Subfamilies identified by the SCI-PHY algorithm can be colored, and EC numbers can be displayed. Large trees can be collapsed to a summary view where terminal nodes represent SCI-PHY subfamilies (using the “Collapse subfamilies” checkbox). Additional functionality is planned.

Below is a PhyloScope display of a tree with collapsed subtrees. All the sequences in a collapsed subtree belong to the single SCI-PHY subfamily shown at the terminal node. The number of sequences in the subtree is shown in brackets. A tooltip lets the user view summary information for each subtree. The path from the terminal tooltipped node to the root is highlighted.

Expanded subtrees are indicated by color.

A great deal of information can be previewed in the tooltip. Clicking the icon takes the user to the corresponding internet resource.