We have developed methods to assign unknown query sequences to species based on known representative sequences from these species. The method will divide posterior probabilities of the assignment among a collection of other potential species. It does this in a statistical decision theory framework. The source code is available from the link below. Currently, due to speed issues, the segregating sites assignment method is preferred.

Segregating Sites Assigner (Download)

Please note that these methods are now ancient and we do not recommend using them.
The methods have been superseded by better methods such as GMYC and BPP.