Nested clade analysis statistics

Abstract Nested clade analysis (NCA) is a flexible and powerful method to study the phylogeography of species and populations, implemented in the software geodis . Despite the popularity of this method, an explicit description of the exact equations used to compute the NCA statistics has never been published. Given the importance of the methodology and increased interest in exactly how it works, here we describe the exact equations implemented in the program geodis for the calculation of these statistics.