A computer program that allows various statistical treatments on microsatellite datasets with null alleles
Current version

All changes since first version are described here


FreeNA is a PC computer program which performs three major tasks on any microsatellite dataset harboring null alleles:

  1.  it estimates null allele frequencies for each locus and population analysed following the Expectation Maximization (EM) algorithm of Dempster, Laird, and Rubin (1977);
  2. it estimates unbiased FST (Weir 1996) following the ENA method described in Chapuis and Estoup (2007);
  3. it calculates the Cavalli-Sforza and Edwards (1967) genetic distance following the INA method described in Chapuis and Estoup (2007).


All methods used in this program are tested and discussed in Chapuis and Estoup (2007).

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If you have any question, please feel free to contact me. However, I strongly recommend you read the manual first.

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Chapuis, M.-P. and Estoup, A. 2007. Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution, 24(3): 621-631. (

Chapuis M.-P., M. Lecoq, Y. Michalakis, A. Loiseau, G. A. Sword, S. Piry, and A. Estoup. 2008. Do outbreaks affect genetic population structure? A worldwide survey in Locusta migratoria, a pest plagued by microsatellite null alleles. Molecular Ecology, 17(16): 3640-3653. (

Last updated

By Marie-Pierre Chapuis and Arnaud Estoup on 2009-11-16