FAQ Asap web: Assemble your Species by Automatic Partitioning

Concerning the method:

Asap is a tool designed to help a biologist to delimitate partitions. A partition is a set of sequences closely related in matter of genetic distance

Asap can handle more than 10000 sequences but the waiting time can be some hours. If you need to work with a big dataset, we recommend that you download the command line to run it on your computer and not overload the server

Fasta format is he most convenient format. If you provide a distance matrix (phylip dnadist or MEGA CSV) you must provide the original length of the sequences
Please rename the ".csv" extension into ".txt" as CSV can be interpretated as special objects by some browsers and will produce unexpected results

Yes you have to download the source here

Concerning results:

On the main Asap page you can tune some parameters. If you have an idea of whats inside your dataset then set in the highlight result section, the lowest to max of distance intraspecific and the highest to min of extra . All results between the two values will be preceded by a star and a blue area will be drawn on the curve . Default values are 0.005(max intra) and 0.05 (min inter)

Asap uses a seed to generate random partitions in order to estimate a partition probability. A new seed can slightly change the values

Some regions are responsive:

Place the mouse over the name and the full name is displayed

Remember that Asap is a tool to help you. We claim that the best partitions will be displayed but the final cut belongs to you.