Non-parametric test for panmixia

The method in brief

The method computes all pairwise differences between all sequences from both samples. It does NOT count indels as differences unless they were recoded (i.e. only when '-' is compared to a '+', it counts as a difference). It then calculates the mean pairwise difference (Ks) and the mean pairwise LOG(1+Diff) (K*s) within each sample. Then, for each replicate, it randomizes the samples (which sequence in which sample) and recomputes those values. The probabilities are the fraction of random samples that have a smaller Ks (or K*s) than the real samples. For more details, please refer to the original paper by Hudson, Boos and Kaplan (1992).

A new version with a graphical output that can take several groups is available. Please visit: http://wwwabi.snv.jussieu.fr/public/mpweb/ it will replace soon this page. any suggestion/comment is more than welcome.

Online version of the test

Please copy/paste your first sample (aligned fasta format)
>seq_a1 GCGAAT-GC >seq_a2 AGGTATTGC >seq_a3 GCGTATTGC

Please copy/paste your second sample (aligned fasta format)
>seq_b1 ATGTATTCA >seq_b2 ACGTATTCA

Please set the number of replicates you would like
Replicates=

Sources

This program has been written in C. It is originally part of a library (libdiversity) of functions that does manage aligned sequences and compute many standard population genetics metrics (The library is available upon request). The source of this stand-alone web-adapted version can be viewed at hudsontest.c (compiled as 'gcc -o hudsontest.cgi -O2 -DMACOSX hudsontest.c -lm'). I would be happy to incorporate any interesting suggestions.

Contacts

If you have any suggestions/comments, please send them to Guillaume Achaz: achaz@abi.snv.jussieu.fr