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
While Asap provides different partitions, score is an indicator of which partition you have to look for. It is combination beetween the two following parameters probability and slope
Proba is the probability that the new found partition is really different that the one found at previous stage . Refer to the publication for more details
Slope is the slope of the curve show on the right at the dist value. A high value means that the neighbours are farer .
Dist is the value used to calculate the slope
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:
A click on one line of the results table: will draw a line on every graphics showing where it cuts the histogram, where it cuts the cumulative ranked distance curve, which value on the asap score curve and where it cuts the dendogram
A click on one node of the dendrogram will color in red all the sequences grouped by the clicked node
Rollover a sequence name on the dendrogram will make appears the full name
Rollover a node will provide some information as: proba is the probablility associated to the considered node, dist distance at which this node was created, nbgroup the number of groups if the partition was done at this stage, node for internal use only and nbunder how many sequences are grouped by this node
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.