K-Estimator is a Windows program to estimate the number of synonymous (Ks) and 
nonsynonymous substitutions (Ka) per site and the confidence intervals by Monte Carlo simulations.  

New features in v.6.0: 
- Synonymous/Nonsynonymous Weight. In codons with two or three changes, 
pathways with synonymous changes now can have a different probability than 
those pathways with nonsynonymous changes.
- The results of simulations to explore Confidence Intervals for Divergence 
estimates, also used to test Ka/Ks>1, are now more detailed. 

Divergence Estimates: 
For noncoding regions, the program can estimate the overall (K) number of nucleotide substitutions per site using several multiple-hits at a site correcting methods: Jukes and Cantorīs 1-parameter (Jukes and Cantor, 1969), Kimuraīs 2-p (Kimura, 1980), Tajima and Nei (Tajima and Nei, 1984), and Tajimaīs 1-p, 2-p and 4-p (Tajima, 1993).  
When coding regions are under analysis, K-Estimator applies the method described in Comeron (1995) to estimate Ks and Ka. This method is a modification of method of Li's (1993) and Pamilo and Bianchi's (1993) (LPB) method that better quantifies the actual number of transitions and transversions and reduces stochastic errors (see Comeron, 1995, for details and comparison to previous methods). Three genetic codes can be applied: Universal, Vertebrate mitochondrial, or Drosophila mitochondrial. Furthermore, three different options can be applied to restrict the codons that are under analysis. 

Confidence Intervals: 
K-Estimator obtains the Confidence Intervals (C.I.) of divergence estimates 
(K for noncoding regions, and Ks and Ka for coding regions) by Monte Carlo simulations. Computer simulations take into account the following parameters: 1) Divergence Value; K or Ks and Ka, 2) number of nucleotides or codons, 3) the transition : transversion (alfa:beta) substitution ratio, and 4) the G+C content for noncoding regions, or the amino acid composition and G+C content at the third position of codons for coding regions. The program can also calculate the exact probability of obtaining any particular divergence value (K for noncoding regions, and Ks, Ka, and Ka/Ks for coding regions). 

K-Estimator also obtains the expected distribution of the ratio Ka/Ks that can be used to detect the action of positive selection (i.e. Ka/Ks significantly >1). In particular, the program generates a condition where the number of nonsynonymous substitutions per nonsynonymous site (Ka) is on average equal to the value estimated for Ks, taking into account all the previous parameters from the analyzed pair of sequences. Therefore, it is obtained the null distribution and C.I. for Ks, Ka and for the ratio Ka/Ks, when the expectation (null hypothesis) for Ka/Ks is =1. The probability of having no STOP codons is also shown.


Good luck,
Josep

http://www.biology.uiowa.edu/comeron
Dept. Biological Sciences
Center for Comparative Genomics
University of Iowa
433 Biology Bldg. (BB)
Iowa City, IA 52242

Tel.:  (319) 335 0628 
Fax:  (319) 335 1069