DnaSP

DnaSP

Version 4.10.9 (September 13, 2006)
DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguadé (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form.

• Windows 95 / 98 / NT / XP
• Macintosh (PowerMac) using SoftWindows or VirtualPC software emulators

• DNA
• SNP

read or write (export) five types of file formats:

• MEGA (Kumar et al. 1994)
• NBRF/PIR (Sidman et al. 1988)
• NEXUS
• FASTA
• PHYLIP
• Arlequin (only write)

In all cases one or more homologous aligned nucleotide (DNA or RNA) sequences should be included in a text file. The total number of sequences and the sequence length that can be handled by DnaSP mainly depend on the available memory, which can analyze data files with a large number (thousands) of sequences of thousands of nucleotides each.

• Rozas, J. and Rozas, R. 1995. DnaSP, DNA sequence polymorphism: an interactive program for estimating Population Genetics parameters from DNA sequence data. Comput. Applic. Biosci. 11: 621-625.
• Rozas, J. and Rozas, R. 1997. DnaSP version 2.0: a novel software package for extensive molecular population genetics analysis. Comput. Applic. Biosci. 13: 307-311.
• Rozas, J. and Rozas, R. 1999. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
• Rozas, J., Sánchez-DelBarrio, J. C., Messeguer, X. and Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.