Marie-Pierre Chapuis & Arnaud Estoup
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).
November 2009, 16th. FreeNA update: the new version replaces the computation of a genotype dataset corrected for null alleles following the INA method and to be used to calculate the Cavalli-Sforza and Edwards (1967) genetic distance by a direct estimation of pairwise values for the Cavalli-Sforza and Edwards (1967) genetic distance following the INA method. This includes the computation of 95% confidence intervals computed by bootstrap procedure. This is because the INA corrected datafile makes the unrealistic assumption of a single null allele state common to all populations. As a result, the use of such a file is strongly discouraged for all population genetics analyses unless carefully testing the performance of such a file for the concerned analysis (see reference Chapuis et al. 2008). Computer simulations showed that the INA correction method provided slightly biased estimates of Cavalli-Sforza and Edwards (1967) genetic distance, but give better estimates than those obtained without correction (Chapuis and Estoup 2007).
Improvements also include removal (i) of a bug in reading genotype datasets with large numbers of loci (although the error was obvious with identical estimates for loci >50, be sure to replace your existing version) and (ii) of limit constraints in numbers of loci and populations that should make FreeNA running for larger datasets.
- 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.
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