DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

• Published in: Molecular biology and evolution Vol. 34; no. 12; pp. 3299 - 3302
• Main Authors: Rozas, Julio, Ferrer-Mata, Albert, Sánchez-DelBarrio, Juan Carlos, Guirao-Rico, Sara, Librado, Pablo, Ramos-Onsins, Sebastián E, Sánchez-Gracia, Alejandro
• Format: Journal Article
• Language: English
• Published: United States Oxford University Press 01.12.2017
• Subjects: Data analysis; Datasets; Deoxyribonucleic acid; DNA; Gene sequencing; Genetic analysis; Genetics; Genomics; Modules; Next-generation sequencing; Nucleotide sequence; Polymorphism; Population (statistical); Population genetics; Simulation; Software; Statistical analysis; Coalescent Simulations; SNPs; VCF; RADseq Analysis; Population Genetics Software
• ISSN: 0737-4038; 1537-1719; 1537-1719
• DOI: 10.1093/molbev/msx248

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.