Neutrality Tests for Sequences with Missing Data

• DOI: 10.1534/genetics.112.139949
• Publication Date: 2012-06-02T04:32:48Z
• Authors: Luca Ferretti; Emanuele Raineri; Sebastian Ramos-O...
• Keywords: Neutrality

Missing data are common in DNA sequences obtained through high-throughput sequencing. Furthermore, samples of low quality or problems the experimental protocol often cause a loss even with traditional sequencing technologies. Here we propose modified estimators variability and neutrality tests that can be naturally applied to missing data, without need remove bases individuals from analysis. Modified statistics include Watterson estimator θW, Tajima's D, Fay Wu's H, HKA. We develop general framework take into account frequency spectrum-based derive exact expression for variance these under neutral model. The proposed here also used as summary describe information contained other classes like microarrays.