A New Efficient Method for Assessing Missing Nucleotides in DNA Sequences in the Framework of a Generic Evolutionary Model

Abstract

The problem of phylogenetic inference from datasets including incomplete characters is among the most relevant issues in systematic biology. In this paper, we propose a new probabilistic method for estimating unknown nucleotides before computing evolutionary distances. It is developed in the framework of the Tamura-Nei evolutionary model (Tamura and Nei (1993)). The proposed strategy is compared, through simulations, to existing methods “Ignoring Missing Sites” (IMS) and “Proportional Distribution of Missing and Ambiguous Bases” (PDMAB) included in the PAUP package (Swofford (2001)).