Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies

Multiperm is a GNU C++ package for shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies. Please refer to our paper:

Parvez Anandam, Elfar Torarinsson and Walter L. Ruzzo, "Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies," Bioinformatics (2009) 25 (5): 668-669. PubMed ID: 19136551.

• supplementary figure S1
• supplementary figure S2

for more details on the algorithm. The source code is available for use under the GPL:

• multiperm-0.9.4.tar.gz (Oct 2010)

Older versions:

• multiperm-0.9.3.tar.gz (Jan 2009)