From the paper:
These results represent a high probability of error, and a bias towards the R* haplogroup, so it is most likely that results based on the haplogroup predictions of these software systems are weakened. For cases in which sex bias in multiethnic populations is estimated by this method, an overestimation of the European component is expected. Haplogroup determination by SNP analysis remains the best approach, considering the low reliability of prediction of software available.This is a very important result, as haplogroup prediction software has sometimes been applied to large collections of Y-STR haplotypes found in the forensic literature. It is important to be cautious about its use, especially for short haplotypes.
The adequate LR+ for the Q1a3a and DE haplogroups could be explained by a lower diversity within each group. Especially in the Q1a3a case, which is a relatively recent haplogroup, the homogeneity is the result of its young evolutionary age, given that the time lapse in which the haplotypes spread away from the haplogroup founder is rather short .
Int J Legal Med. 2010 Jan 15. [Epub ahead of print]
Software for Y-haplogroup predictions: a word of caution.
Muzzio M, Ramallo V, Motti JM, Santos MR, López Camelo JS, Bailliet G.
The development of online software designed for genetic studies has been exponentially growing, providing numerous benefits to the scientific community. However, they should be used with care, since some require adjustments. The efficiency of two programs for haplogroup prediction was tested with 119 samples of known haplotypes and haplogroups from Argentine populations. Quantitative estimates of the predictive quality of both software systems were computed with the uncertainty coefficient; and sensitivity, specificity, positive, and negative likelihood ratios were also calculated to assert the reliability of both programs, showing high probabilities of assigning an incorrect haplogroup.