Before you start

Something to be aware of is that data files are usually saved as you go along. This means that results can accessed in a more interactive manner. The way that this works is by using the file name of your alignment file as an identifier. This is very simple and effective system but can come unstuck if you reuse file names. Please make sure that you choose unique filenames. Otherwise results can be recalculated from scratch using the -u flag available in each of the scripts.