NG-NEW A Modified Nei-Gojobori Method for Computing Synonymous and Nonsynonymous Distances
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NG-NEW Tags

sequence DNA sequence DNA nucleotide rate of nonsynonymous find patristic distances synonymous distance nonsynonymous distance radical nonsynonymous distance Synonymous Substitution Nonsynonymous Substitution Modified Rational Method synonymous

NG-NEW Description

The NG-NEW application was developed a small command line tool for estimating synonymous and nonsynonymous distances between protein coding DNA sequences. The method is modified from the original Nei and Gojobori (1986) method to take into account the transition bias. To use the program, you need an input file containing the protein coding DNA sequences (see rnase.seq for an example). This file begins with two numbers: the number of sequences and the number of nucleotides per sequence (sequence length). The second line will be the name of the first sequence, and the third line will be the first sequence, and so on. Only A, G, C, T, a, g, c, and t are allowed. Gaps should be removed and sequences should be aligned beforehand. The sequences should only include protein-coding regions, with stop codons removed.

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