DnaSP v.4

DnaSP version 4.90
Julio Rozas et al.

DNA Divergence Between Populations module. If you perform analysis in a selected region DnaSP will incorrectly calculate the total number of fixed differences. DnaSP will show the total number of fixed differences for the total region.
Synonymous and Nonsynonymous substitutions module. If you have a sequence data set with positions with alignment gaps or missing data in the coding region, DnaSP will incorrectly form the codons. In this case, DnaSP will incorrectly estimate various parameters.

DNA Divergence Between Populations module. In some rare cases DnaSP does not calculate the parameter Da (Nei 1987, equation 10.21).
Population Size Change module. Bugs found in the printer option.

Polymorphic Sites File module. DnaSP does not calculate the number of synonymous and nonsynonymous substitutions if the original data file is File#2.
Export Data File As PHYLIP format. DnaSP generates a PHYLIP data file that some computer programs can not read (but it is right).
DNA Polymorphism module. For a large data set, DnaSP crashes after computing the variance of the nucleotide diversity.
Data Menu || Filter / Remove Positions module; Coding Positons option. For a data file with truncated codons, DnaSP removes incorrectly the non coding positions.
Data Menu || Assign Genetic Code. In some rare cases, with two opened data files, DnaSP assigns incorrectly the codons.

In spite that DnaSP runs quite well in Macintosh with Virtual-PC, a user (C. Robin; University of Melbourne) reported a Virtual-PC emulator problem affecting the HKA module.

Gene Flow and Genetic Differentiation Module | Sites with alignment gaps option (2, considered; 3, excluded in pairwise comparisons). In some cases, DnaSP gives incorrect values of Kxy. Please check your results.