DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

TLDR

Version 6 of DnaSP is introduced as an updated tool for exhaustive population‑genetic analyses on multiple sequence alignments. The upgrade adds modules for genomic‑partitioning data, scalable high‑throughput analysis, multi‑locus statistics, and coalescent simulations across diverse demographic scenarios. The fully documented software is freely available at http://www.ub.edu/dnasp.

Abstract

We present version 6 of the DNA Sequence Polymorphism (DnaSP) software, a new version of the popular tool for performing exhaustive population genetic analyses on multiple sequence alignments. This major upgrade incorporates novel functionalities to analyze large data sets, such as those generated by high-throughput sequencing technologies. Among other features, DnaSP 6 implements: 1) modules for reading and analyzing data from genomic partitioning methods, such as RADseq or hybrid enrichment approaches, 2) faster methods scalable for high-throughput sequencing data, and 3) summary statistics for the analysis of multi-locus population genetics data. Furthermore, DnaSP 6 includes novel modules to perform single- and multi-locus coalescent simulations under a wide range of demographic scenarios. The DnaSP 6 program, with extensive documentation, is freely available at http://www.ub.edu/dnasp.