This paper presents the design and evaluation of a task allocation framework for Biological Sequence Comparison applications that use dynamic programming and run in heterogeneous environments. The framework is composed by four modules and either task allocation policies or applications can be integrated to it. The results obtained with four different task allocation policies in a 10-machine heterogeneous environment show that, for some sequence sizes, we were able to reduce the execution time of the parallel application in 54.2%, with the appropriate allocation policy.