SCANMS: adjusting for multiple comparisons in sliding window neutrality tests

SCANMS: adjusting for multiple comparisons in sliding window neutrality tests

SUMMARY A Perl utility called SCANMS was written that operates on parametric bootstrap data generated by Hudson's simulator MS. SCANMS simulates sliding window analysis of Tajima's D or Fu and Li's D(*) or F(*) over the replicates and generates the empirical joint distribution of window minima and maxima. This distribution may then be used to calculate achieved significance values or significan...

Adjusting for Multiple Comparisons in Decision Tree Pruning

Introduction Bonferroni Pruning Pruning is a common technique to avoid over tting in decision trees. Most pruning techniques do not account for one important factor | multiple comparisons. Multiple comparisons occur when an induction algorithm examines several candidate models and selects the one that best accords with the data. Making multiple comparisons produces incorrect inferences about mo...

Neutrality tests using DNA polymorphism from multiple samples.

The polymorphism of a gene or a locus is studied with increasing frequency by multiple laboratories or the same group at different times. Such practice results in polymorphism being revealed by different samples at different regions of the locus. Tests of neutrality have been widely conducted for polymorphism data but commonly used statistical tests cannot be applied directly to such data. This...

Tests of Neutrality

Neutrality tests for sequences with missing data.

Missing data are common in DNA sequences obtained through high-throughput sequencing. Furthermore, samples of low quality or problems in the experimental protocol often cause a loss of data even with traditional sequencing technologies. Here we propose modified estimators of variability and neutrality tests that can be naturally applied to sequences with missing data, without the need to remove...