SAP identifies species and other taxonomic units from DNA sequences. It uses Bayesian phylogentics to evaluate the statistical support for assignment to each taxonomic unit represented by sequences in a database like GenBank.
The command line version of SAP is available for Linux/Unix plaforms as well as OSX and Windows. You can compile the sourcecode, but prebuilt versions for Windows are also available.
You can try out SAP without installing it locally by visiting the web server. The capacity of the server is limited, but please let me know if you would like to run large analyses on the web server.
Say you have retrieved COI sequences from an environmnetal sample and want to know which taxonomic groups these can be assigned to. Use SAP to produce a taxonomic assignment to the finest reliable level.