DnaSP Bugs Reports (DnaSP Version 4)

Bugs detected in older versions

Bug detected in version 4.0.3 (or earlier versions), fixed in version 4.0.4

• Reverse Complement Data File. In some cases, DnaSP generates an incorrect reverse complement data file. Please check your results.

Bug detected in version 4.0.4 (or earlier versions), fixed in later versions

• Gene Flow and Genetic Differentiation Module | Sites with alignment gaps option (2, considered; 3, excluded in pairwise comparisons). Estimates of Snn statistic might be incorrect. Please check your results. [Bug reported by D. Toleno; UC Riverside].

Bugs detected in version 4.0.5 (or earlier versions), fixed in later versions

• Gene Flow and Genetic Differentiation Module. The P-value (Permutation test) for the Snn statistic could be slightly incorrect. [Bug reported by Todd A. Schlenke; Cornell University].
• Linkage Disequilibrium. Estimates of Wall's Q statistic are incorrect. Please check your results. [Bug reported by M. Macpherson and D. Witten; Stanford University].

Bugs detected in version 4.0.7 (or earlier versions), fixed in later versions

• Haplotype Data File Modules | Sites with alignment gaps option (2, considered; 3, Only gaps are considered). In presence of missing data, DnaSP might generate erroneous haplotype data. Please check your results. [Bug reported by M. Heuertz; Université Libre de Bruxelles].
• Gene Flow and Genetic Differentiation Module | Sites with alignment gaps option (2, considered; 3, excluded in pairwise comparisons). Estimates of the number of segregating sites might be incorrect. Please check your results. [Bug reported by M. Aguadé; Universitat de Barcelona].

Bug detected in version 4.10.9 (or earlier versions); fixed in version 4.20.1

• Gene Flow and Genetic Differentiation Module | Sites with alignment gaps option (2, considered; 3, excluded in pairwise comparisons). Estimates of the number of segregating sites might be incorrect. Please check your results. [Bug reported by Scott Glaberman; Yale University].

Bug detected in version 4.10.9 (or earlier versions); pending to be fixed

• Running DnaSP in Linux using Wine. In some cases, the sign of the negative values are not displayed (this is a Wine bug). Please, it is very important that you check your results. [Bug reported by Albert Vilella; EBI].

Bug detected in version 4.50.2 (or earlier versions); fixed in version 4.90

• DNA Divergence Between Populations | Compute Variances of Dxy and Da option. These estimates might be incorrect. Please check your results. [Bug reported by Alicia Amadoz and Fernando Gonzalez-Candelas; Universitat de València].

Bug detected in version 4.90.1; fixed in version 5.00.04

• Open Unphase/Genotype Data File | Haplotype reconstruction using PHASE and HAPAR methods. Occasionally DnaSP crashes after running this command (without any warning).

Bug detected in version 5.00.7 (or earlier versions); fixed in version 5.10.00

• Fu and Li's (and other) Tests with an Outgroup | Estimates of the normalized Fay and Wu'H might be incorrect in the presence of ambiguous information in the outgroup. Please check your results. [Bug reported by S. E. Ramos-Onsins; Universitat Autònoma de Barcelona].

September 7, 2009
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