:: DESCRIPTION
Syn-SCAN calculates the synonymous and nonsynonmous mutation rates between sequences containing ambiguous nucleotides
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN).
Gonzales MJ, Dugan JM, Shafer RW.
Bioinformatics. 2002 Jun;18(6):886-7.
:: DESCRIPTION
SNAP calculates synonymous and non-synonymous substitution rates based on a set of codon-aligned nucleotide sequences. It outputs a synonymous and a non-synonymous distance matrix, an exhaustive pairwise codon-by-codon comparison, and a summary table.
::DEVELOPER
Bette Korber at Los Alamos National Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Korber B. (2000)
HIV Signature and Sequence Variation Analysis.
Computational Analysis of HIV Molecular Sequences, Chapter 4, pages 55-72.
Allen G. Rodrigo and Gerald H. Learn, eds. Dordrecht, Netherlands: Kluwer Academic Publishers.
:: DESCRIPTION
BN-BS is a software to estimate branch lengths in terms of synonymous and nonsynonymous substitutions per site, while the tree topology is given. The program uses the modified Nei-Gojobori method (Zhang et al. 1998) to estimate pairwise synonymous and nonsynonymous distances among present-sequences and then estimates branch lengths and their variances by using the ordinary least-squares method.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Zhang J., H. F. Rosenberg, and M. Nei (1998)
Positive Darwinian selection after gene duplication in primate ribonuclease genes.
Proc. Natl. Acad. Sci. USA 95:3708-3713.
