DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented methods allow for: (i) analyses on multiple data files, (ii) haplotype phasing, (iii) analyses on insertion/deletion polymorphism data, (iv) visualizing sliding window results integrated with available genome annotations in the UCSC browser.