Hi, Ks value is used as crude measurement of time of duplication. Higher the value of Ks longer the time since duplication. Can someone tell me what if we get Ks value in negative (for example -0.11)?
From my quick web and literature search it seems that Ks, the synonymous substitution rate, is always > 0. So if you get negative Ks, what it means is that you've made an error in your calculation.
This project at Google Code has lots of documentation and might be useful.
Identical sequences by definition can have no synonymous substitutions and thus Ks=0. As genes (duplicates) diverge they accumulate mutations, some of which are fixed. Fixed changes at synonymous sites contribute to Ks so Ks increases over time. It is clear by thinking about the process of mutation accumulation that Ks cannot be negative-- sequences cannot have negative mutations.
However, if you are calculating Ks on a tree and there are high levels of convergence or reversions or concerted evolution, some branches may be ascribed a negative length (Ks) in order to make the math work. This can also arise if your sequences have errors.
It is a good idea to think in terms of substitutions and mutations (which are differetn) and not time. Time is related to Ks only by a variety of assumptions.
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Which model did you use to calculate Ks? Usually Ks can't be negative, using common methods like Nei and Gojobori 1986 or Li 1993.