HON-NEW

The HON-NEW application was designed for estimating conservative and radical nonsynonymous distances between protein coding DNA sequences. The method is modified from the original method of Hughes, Ota, and Nei (1990)by taking into account the transition bias.

Three types of amino acid classifications (charge, polarity and that of Miyata and Yasunaga) are provided. One can also define conservative and radical amino acid changes by oneself.

One can define amino acid groups so that changes among groups are radical and within groups are conservative. To do that, creat a file named self.div. In this file, the first line should be the groups of amino acids (e.g., in the case of charge, there are three groups [-,0,+]), the second line is the number of amino acids in the first group, a space, and the amino acids in the group.

One-letter code of amino acids should be used. Next line will be the information for the second group. One only needs to input the information of the first n-1 groups, if there are n groups in total, because the last group can be derived from the information of the first n-1 groups.