DNAsp 


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DnaSP is a software package for Windows that performs extensive population genetics analyses from DNA sequence data. DnaSP estimates several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites), linkage disequilibrium, recombination, gene flow and gene conversion. DnaSP can also carry out several tests of neutrality: those of 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. DnaSP estimates i) the average number of nucleotide differences per site between two sequences, or nucleotide diversity, Pi (Nei 1987), and its sampling variance and standard error (Nei 1987); ii) the nucleotide diversity using the Jukes and Cantor correction (Jukes and Cantor 1969; Lynch and Crease 1990); iii) the nucleotide diversity by pairwise-deletion; iv) the average number of nucleotide differences, k (Tajima 1983) and its stochastic, and sampling variances (Tajima 1993); v) Theta = 4Nu, where N is the effective population size, and u is the mutation rate per nucleotide (or per sequence) and per generation (Nei 1987; Tajima 1993) and its variance for free and for no recombination (Tajima 1993); vi) Theta per nucleotide under the finite sites model (Tajima 1996). This program estimates Ka (the number of nonsynonymous substitutions per nonsynonymous site), and Ks (the number of synonymous substitutions per synonymous site) for any pair of sequences (Nei and Gojobori 1986, equations 1-3). DnaSP can estimate the nucleotide diversity for synonymous, nonsynonymous and silent (both synonymous and noncoding positions) sites. (http://www.ub.edu/dnasp/DnaSP32Inf.html ).