See the FAQ if you want to learn everything on this script

The methodology is explained in Achaz G, Palmer S, Kearney M, Maldarelli F, Mellors JW, Coffin JM, Wakeley J. (2004) Mol Biol Evol. 21(10):1902-12
The syntax of your sequence names must take into account that there are subpopulations in the set.
In order to discreminate automatically the different groups If not a chronological serie, the order in which the populations appear in the fasta alignment is important for the graphic representation. The different populations names are taken in order of seen in the alignment and are spotted in the same order on the graphic. You can change this order if needed at the end of the form, you have to add at this end of each sequence name, separated by a semicolon, the name of the population.

e.g.: for a sequence belonging to pop 1
if your data are chronological, choose a int value at end of pop name and separate it from the name by a dot (ex here day=136)

For now, sites with indels are completely ignored.

Paste your alignment here (FASTA format):

Number of permutations: Chronological series If checked, populations are automatically sorted on numerical value in population name eg xxx;day.136 and xxx;day.89 will sort sequences belonging to day.89 before those belonging to day.136

Group order You can provide an order in which you want to consider the different populations. Different populations should be separated by : If empty the order will be the order encoutered in file if needed