KarlinAltschul statistics provide a theory for computing the probability that a local alignment of a given score will be found between two random sequences of the same lengths as the query and database sequences. For an introduction, see this page on the NCBI web site. The probability is often expressed as an expectation value, abbreviated to Evalue. KA statistics apply to local alignments only; Evalues cannot be computed for global alignments. According to KA statistics, the expectation value E for a local alignment with score S is: E = K q d exp(LS) Here, q is the query sequence length, d is the database size in letters, exp is the exponential function and K and L are parameters derived from the alignment scoring parameters. L is called the Lambda parameter. USEARCH does not automatically adjust the K and Lambda parameters if the alignment scoring parameters are changed  they must be provided on the command line.
