The ProPhylER Interface

The Interface is a Java Applet. An applet is a program that is loaded from the server into your computer and runs on your computer. Its 'host' is your browser.

You must have a very recent version of Java on your computer, and you should use a well-maintained browser such as Safari or Firefox.

Loading an Interface Session

Loading a Session happens in three stages: First the applet is loaded from the ProPhylER server onto your computer and begins to run there. Once it runs, it transfers the data for the cluster from the ProPhylER server into memory on your computer. Finally, the applet parses the data and displays it graphically.

After the applet has loaded, and before it loads the data, you will be asked to "Trust" a Security Certificate. This is necessary because the applet needs permission to write data to your computer if and when you decide to save data such as the alignment or the data table.

Loading Time varies depending on your connection speed and the size of the cluster. Once the applet has loaded the data, everything is very fast because it all happens on your computer, with no more interaction with the ProPhylER server.

Navigating the Interface

Role of the Reference Sequence

The reference sequence is that sequence according to which the data are displayed. Because ProPhylER's analyses are based on alignments and not on individual sequences, any sequence in the alignment can serve as the reference sequence. The underlying data do not change when you change the reference sequence, only the display changes.

If you work on a particular protein from a particular species you should make it the reference sequence, if ProPhylER has it. Your initial search (by Blast or database ID) may have specified your sequence as the reference sequence automatically.

You can change the reference sequence in the Selector tab of the Interface.

Substructure in ProPhylER Alignments

Understanding the substructure of ProPhylER alignments is extremely important to avoid confusion, so here is a separate help page on Cluster Subsets and Phylogenetic Scope.

Quick Help Views and Further Explanations

The links below point to a set of pages that contain the Quick Help views you will see when you click on the Quick Help tab of the Interface. Each page has further explanations that are not available in the limited space of the Quick Help tab. Each will open in a separate window.

Main View | Gene Tree | Taxonomy | Selector | Downloads

Annoyances

Three things about the interface are certain to annoy you:

• You cannot resize it. It is about 950x640 pixels and you just can't change that.
• The mouse roller wheel does not work.
• Navigating the Gene Trees and Taxonomies is a little cumbersome.

We do hope to fix these issues at some point in the future ...