The Phylip package is a very powerful tool that often has its own way of doing things. As a result, this type of analysis can be very time consuming. Even with the platform that SACS uses, analysis runs on data sets can take days or even weeks.

In this initial phase of getting the Phylip package running on the web, we tried to make sure there were no runaway processes filling your disk with the screen trace files which ask for the name of the necessary input file. Further effort will be put into determining the size ratio between data files running as interactive jobs and files that run in the background sending results as email messages. Information also needs to be gathered about just how long a person is willing to wait on the web for results.

Of the programs currently online, the only flow combinations using multiple data sets are those that call for a neighbor run. In these cases, the number of replicates is fixed at 100. While seqboot can generate multiple data sets, none of the other programs can use them. In the flow combinations, there is no way to select the out group since this changes from output file to output file during the flow process.

After the final trees have been produced, they can then have their branches rearranged interactively with the Phylip program retree.

Data generated by these web programs will go to the /usr/tmp/phylip location on socrates. Be sure to name your runs, in order that they may be more easily found there.

These pages were developed on a MAC, so Windows users might encounter some problems. In case you do, please contact Susan Johns with exact information about the nature of the problem discovered.