Test for evidence of genetically segregated populations, using a "detuned" version of the Slatkin-Maddison test.
This analysis implements canonical and modified versions of the Slatkin-Maddison phylogeny based test for population segregation. The test estimates the minimum number of migration events using maximum parsimony, and then evaluating whether or not this number is lower than expected in a panmictic or unstructured population using permutation tests
Note: assumes that leaf names that can be partitioned into sets using regular expressions
For example
((((((((x_US_x_A_01C:0.0125396,(((((x_US_x_A_01P:0.00887628,(( x_US_x_A_08P:-0.000190918,x_US_x_A_11P:0.00313157):0.0106883, x_US_x_A_14C:0.0103815):0.00311658):0.00120812,x_US_x_A_09P:0.00320468): 0.0108828,x_US_x_A_12P:0.00732672):0.00596663,x_US_x_A_07C:0.00449846):0 .00639319,((((x_US_x_A_02P:-2.62303e-05,x_US_x_A_05P:0.00591507):0. 000156788,x_US_x_A_04P:0.00576826):0.00907366,((x_US_x_A_03P:0.00941548, x_US_x_A_14P:0.00866127):0.00229499,x_US_x_A_13P:0.0209192):0.00469629): 0.0146758,(x_US_x_A_10P:0.000156443,x_US_x_A_15P:0.00578946):0.00472532) :0.0103079):0.00733948):0.00228489,x_US_x_A_06P:0.00557974):0.00472981, x_US_x_A_04C:0.00478858):0.00105548,x_US_x_A_05C:0.0120259):0.0060905, x_US_x_A_12C:0.002911):2.90824e-05,x_US_x_A_11C:-5.79432e-06):4.34574e- 06,x_US_x_A_13C:-4.34574e-06):4.34574e-06,((x_US_x_A_08C:0.0029538, x_US_x_A_09C:-1.31511e-05):0.00296627,x_US_x_A_10C:-8.69148e-06):4. 34574e-06,x_US_x_A_15C:-4.34574e-06);
Which can be partitioned into two groups of leaves, those that end in "P", and those that end in "C"
A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
A custom visualization module for viewing these results is available (see http://vision.hyphy.org/Slatkin for an example)