Functional evolution is often driven by positive natural selection. Although it 
is thought to be rare in evolution at the molecular level, its effects may be 
observed as the accelerated evolutionary rates. Therefore one of the effective 
ways to identify functional evolution is to identify accelerated evolution. Many 
methods have been developed to test the statistical significance of the 
accelerated evolutionary rate by comparison with the appropriate reference rate. 
The rates of synonymous substitution are one of the most useful and popular 
references, especially for large-scale analyses. On the other hand, these rates 
are applicable only to a limited evolutionary time period because they saturate 
quickly--i.e., multiple substitutions happen frequently because of the lower 
functional constraint. The relative rate test is an alternative method. This 
technique has an advantage in terms of the saturation effect but is not 
sufficiently powerful when the evolutionary rate differs considerably among 
phylogenetic lineages. For the aim to provide a universal reference tree, we 
propose a method to construct a standardized tree which serves as the reference 
for accelerated evolutionary rate. The method is based upon multiple molecular 
phylogenies of single genes with the aim of providing higher reliability. The 
tree has averaged and normalized branch lengths with standard deviations for 
statistical neutrality limits. The standard deviation also suggests the 
reliability level of the branch order. The resulting tree serves as a reference 
tree for the reliability level of the branch order and the test of evolutionary 
rate acceleration even when some of the species lineages show an accelerated 
evolutionary rate for most of their genes due to bottlenecking and other 
effects.