Shufflet: Shuffling sequences while conserving the k-let counts

Abstract

Shufflet is a program and a web-application that generates fast random shufflings of sequences (DNA, protein or others), conserving the exact k-let counts for a given k. The sequences are sampled uniformly from all the valid permutations. Availability: As a web application: http://www.genetique.uvsq.fr/eivind/shufflet.html. Source code is available on request for academic use.