a.) You can specifiy the startup path for the save-file or load-file dialogs. This can be very handy and save a lot of time spent with clicking around through extensivly branched directory trees.

b.) The columns of an PanGEA analysis may be separated by different characters. This applies for the 'Manage pairwise alignments' and 'Manage SNP' analysis. If you want to copy and paste the results into a spreadsheat program like MS Excel the most convenient way is to enter a tabulator key as separating character and just copy and paste the results into the application.

c.) If you want to identify SNPs from a many pairwise alignments it is not possible to load them all at once into the memory. The process has been done in a stepwise manner. The value in the textbox refers to the stepsize. A large stepsize means that the memory (RAM) requirements will be high but computation will be fast and vice versa. Per default 50 000 pairwise alignments will be analyzed at once, this should be fine in most cases, if you encounter a out of memory exception during SNP-identification decrease this value.