Forest Genetics and Forest Tree Breeding


Software for Analysis of Haplotype Data - version 1.05 -

Copyright 2009 Nicolas-George H. Eliades and Demetrios G. Eliades. Emails and/or URL


HAPLOTYPE ANALYSIS is a new software for analysis of data from organelle genomes (chloroplast or mitochondrial) which are observed from microsatellites (SSR) or PCR-RFLP markers. The main advantage of this software is that the analysis is performed based on the frequency of haplotypes, which was identified by combining the size variants at the investigated microsatellites (SSR) loci or by combining the restricted fragments of PCR-RFLP loci. The analysis initiates by estimating haplotype frequencies in each population, and in continuation it calculates genetic diversity within each population (intra-population analysis) by

  • the number of different haplotypes (A)
  • the number of private haplotypes (Ph)
  • the effective number of haplotypes (Ne)
  • the haplotypic richness (HR) was estimated using the rarefaction method (El Mousadik and Petit, 1996)
  • Nei's index of genetic diversity (HE) estimated without bias (Nei, 1973)
  • the mean genetic distance between individuals (Dsh2) only for cpSSR (Goldstein et al., 1995)

  • NOTE: For microsatellite markers (chloroplast, mitochondrial) the average genetic distances among the individuals within datasets were estimated using the value of Dsh2 (Goldstein et al., 1995), based on the average squared sum of all length differences at microsatellites and with the assumption of the stepwise mutation model (Morgante et al., 1998).

    Population genetic structure from the population samples (inter-population analysis) is computed utilizing

  • Nei's minimum genetic distance (Nei, 1987)
  • Genetic differentiation among the populations and contribution of each of them to the total diversity (Finkeldey & Murillo, 1999)

  • Disclaimer

    HAPLOTYPE ANALYSIS v1.0b is a first test version of software written in Visual Basic for Applications (VBA) within Excel. On the PC, it is compatible with Excel 97 upwards under Windows 95, 98 and 2000, while it has been extensively tested and run in Excel 2002 and Excel 2003 under Windows XP. This first version is possible to contain bugs, some of which are probably easy to detect. However, the authors would appreciate to be informed of any detected bug; in which case please send a sample data file and type of software used, while any suggestions for improvement of the scope and/or of the functionality of the program are welcome (Email and/or


    Download software and User's Manual as the zipped file


    • El Mousadik A, Petit RJ (1996). High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theoretical and Applied Genetics: 92, 832-839.
    • Finkeldey R, Murillo O (1999). Contributions of subpopulations to total gene diversity. Theoretical and Applied Genetics: 98, 664-668.
    • Goldstein DB, Linares AR, Cavallisforza LL, Feldman MW (1995). An evaluation of genetic distances for use with microsatellite loci. Genetics: 139, 463-471.
    • Hurlbert SH (1971). The nonconcept of species diversity: a critique and alternative and alternative parameters. Ecology: 52, 577-586.
    • Morgante M, Felice N, Vendramin GG (1998) Analysis of hypervariable chloroplast microsatellites in Pinus halepensis reveals a dramatic bottleneck. In: Karp A eds Molecular tools for screening biodiversity: plants and animals, Chapman and Hall, London, pp. 402-412.
    • Nei M (1973). Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci. USA, 70, 3321-3323.
    • Nei M (1987). Molecular Evolutionary Genetics. New York, Columbia University Press, pp. 219-220.
    • Petit RJ (2003). Manuscript of RAREFAC.


    Eliades N-G., Eliades D. G. (2009). HAPLOTYPE ANALYSIS: Software for analysis of haplotype data. Distributed by the authors. Forest Genetics and Forest Tree Breeding, Georg-August University Goettingen, Germany. URL

    HAPLOTYPE ANALYSIS is free software: you can redistribute it under the terms of the GNU General Public License (GPL) v.3, as published by the Free Software Foundation. HAPLOTYPE ANALYSIS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of merchantability or fitness for a particular purpose. Reassembling is not permitted. See the GNU General Public License, a copy of which is contained in the file "gpl.txt" included in the download file, or see