Sliding Window Analysis of KA and KS Web Server
Credits
This web server is created and maintained by Han Liang in the Landweber group in the Department of Ecology & Evolutionary Biology at Princeton University.
Citation:
In citing the SWAKK web server, please refer to:
Han Liang, Weihua Zhou and Laura F. Landweber (2006)
SWAKK: a web server for detecting positive selection using a sliding window substitution rate analysis
Nucleic Acids Research 34(Web Server Issue) W382-4
Main References:
1.Li, W.H., Wu, C.I. and Luo, C.C. (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol, 2, 150-174.
2.Nei, M. and Gojobori, T. (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol, 3, 418-426.
3.Li, W.H. (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol, 36, 96-99.
4.Yang, Z. and Nielsen, R. (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol, 17, 32-43.
5.Endo, T., Ikeo, K. and Gojobori, T. (1996) Large-scale search for genes on which positive selection may operate. Mol Biol Evol, 13, 685-690.
6.Berglund, A.C., Wallner, B., Elofsson, A. and Liberles, D.A. (2005) Tertiary windowing to detect positive diversifying selection. J Mol Evol, 60, 499-504.
7.Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res, 22, 4673-4680.
8.Yang, Z. (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci, 13, 555-556.
Acknowlengments:
This work was supported by National Institute of General Medical Sciences grant GM59708 and National Science Foundation grant DBI-9875184 to L.F.L.
If you have any questions about this web server, please email Han Liang at the University of Chicago.
Copyright@2006