By applying standard statical tools. 

You can control systematic error with the proper model of sequence evolution - use some model choice program to help you identify the best model. However, because sequence evolution follows a Poisson process, the random error (standard deviation) with increase with time back to the common ancestor (mean) and will always be quite large (a Poisson mean equals the standard deviation), Nevertheless you do have control over reducing the systematic error so do that at least.