Welcome to the CISN website
CISN: a software for confidence intervals of the
              nucleotide substitution number

A major task in the exploration of an evolutionary process is to estimate the substitution number per site of a protein or DNA sequence. The confidence interval approach for estimating the substitution number can provide a more precise estimation than the point estimation. Recently, useful confidence intervals have been constructed for estimating the nucleotide substitution number. By applying the confidence interval procedure, we first need to align sequences, and then apply the procedure on the aligned sequences. Therefore, to develop a program which can combine both techniques to provide a convenient tool for nucleotide substitution number estimation is essential. In this study, we develop an R program to provide an easy way for the nucleotide substitution number estimation which integrates the alignment procedure of Bioconductor software and R codes of the confidence interval procedure. This integrated program can obtain 5 different confidence intervals for the nucleotide substitution number by comparing two nucleotide sequences. Moreover, it is likely that empirical information may exist in real application that the substitution number may be within a specific range. In order to broaden the applicability of the program, we associate the empirical information with the observed data in the program to obtain more reliable confidence intervals, which can provide more precise information for the nucleotide substitution number.

◆   Evolutionary Models

●    JC69 model (Jukes and Cantor, 1969) (CISN-JC69)
●    K80 model (Kimura, 1980) (under investigation)     
●    F81 model (Felsenstein, 1981) (under investigation)   
●    HKY85 model (Hasegawa, Kishino and Yano, 1985) (under investigation)
●    T92 model (Tamura, 1992) (under investigation)
●    TN93 model (Tamura and Nei, 1993) (under investigation)
●    GTR: Generalised time-reversible (Tavaré, 1986) (under investigation)

◆   Reference

●    Wang, H. (2011). Confidence Intervals for the Substitution Number in the
       Nucleotide Substitution Models. Molecular Phylogenetics Evolution, 60,
       472-479.
●    Wang, H., Tzeng, Y.H. and Li, W.H. (2008). Improved variance estimators
       for one- and two-parameter models of nucleotide substitution. Journal of
       Theoretical Biology, 254, 164-167.

●    Wang, H. and Chen, W.S. CISN-JC69: an integrated program for confidence
       intervals of the nucleotide substitution number for JC69 model. Submitted.

◆   Download the R-codes

	Download link	File type	File size	Update
R codes	CISN-JC69	txt	9.95KB	2013.04.15

The R project web for free download is http://www.r-project.org.

Please ensure you already have installed R to run CISN codes.

◆   Run the code.

◆   R code user manual.

◆   A data Example

Data source:
●    J.P. Dumbacher, T.K. Pratt, and R.C. Fleischer, (2003). Phylogeny of the
      owlet-nightjars (Aves: Aegothelidae) based on mitochondrial DNA sequence,
      Molecular Phylogenetics Evolution, 29,  540-549.
●    Wang, H. and Hung, S.L. (2012). Phylogenetic tree selection by the adjusted
       K-means approach. Journal of Applied Statistics, 39, 643-655.

The data set for the genome of the 11 owlet-nightjars.

	Download link	File type	File size	Update
Data file	DATA	rar	4.26KB	2012.12.11

　

Figure. A simple form of the tree for the avian family Aegothelidae of the above data set.

◆   Contact

If you have any questions on CISN codes, please feel free to contact us at
wang@stat.nctu.edu.tw. We welcome your feedback and comments.