The pstogif utility was also used to convert the postscript output from the phylip tree drawing programs. The information from the user's selection of options is used to automatically generate a perl script, to wrap all the management as a singel job. Jobs are handled in batch queueing system which obviously reduces the impact of a user wishing to conduct various types of analysis simultaneously. The results are simply stored in Unix directories and files. Intermediary files are in a scratch area and only the required files are moved into the user's directory upon the job completion.
Lets assume that a user is interested in the phylogeny of flavodoxin protein sequences.
He has carried out keyword and sequence similarity searches and found appropriate sequences. An automatic sequence alignment has been done and edited using the user's biological knowledge. PIE is then selected from the HGMP-RC WWW menu. After the foresight of attending a phylogeny course, the user wishes to choose a maximum likelihood method and checks the online help in PIE as a reminder. The below screen shots illustrate a typical choice.