FAQ ASAP web: Assemble Species by Automatic Partitioning

Concerning the method:

ASAP is a tool designed to propose partitions of species hypotheses using genetic distances calculated between DNA sequences.

ASAP can handle more than 10 000 sequences, but the computation time can be quite important in this case (several hours). If you need to work with a very large dataset, we recommend you to download the command line version of ASAP to run it on your computer instead of overloading the server.

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

Yes, you can download the source code here

Concerning results:

On the main ASAP page you can tune some parameters (see the help page). All the partitions within the range of genetic distances you provided will be preceded by a star and a blue area corresponding to this range will be drawn on the curve. Default values are 0.005 and 0.05.

For each partition and for each node for which a probability has been calculated, the darker the color of the dots and squares, the higher the probability. When the probability was not computed, the square is grey. We choose to use different symbols (dots and squares) for the table and the curve in one hand and for the dendrogram in the other hand, because the probability is not calculated the same way. For the table and the curve, it corresponds to the probability of the partition. For the dendrogram, it corresponds to the probability that merging the groups within the node is compatible with the known distances inside each of these groups. A very low probability (dark color) indicates that this group is unlikely, i.e. that the groups within this node probably correspond to different species. . Please refer to the publication for more details.

ASAP uses a seed to generate random partitions in order to estimate the probability of a partition. A new seed can slightly change the probabilities.

Some regions are responsive:

Roll over the name and the full label will be displayed

Remember that ASAP is an exploratory tool designed to identify the best partitions of species, given the criteria used by ASAP (in particular the genetic distances). Your own species hypotheses might be based on other data, methods or criteria of species delimitation, and might thus be different from the best ASAP partitions. Combining all these results in an integrative taxonomy approach is generally a good idea.