Using uniformat and gene[rate] to analyze data with ambiguities in population genetics

Abstract

Some genetic systems frequently present ambiguous data that cannot be straightforwardly analyzed with common methods of population genetics. Two possibilities arise to analyze such data: one is the arbitrary simplification of the data and the other is the development of methods adapted to such ambiguous data. In this article, we present an attempt at such a development, the uniformat grammar and the gene[rate] tools, highlighting the specific aspects and the adaptations required to analyze ambiguous nominal data in population genetics.