ap_PairwiseSequenceIdentityProtocol evaluates pairwise sequence identity between all sequences found in a given FASTA file.
The calculated values are printed on the screen if they are greater than a given cutoff (third parameters, 0.25 in the example below). Calculations may be executed in several parallel threads, the number of threads is the second parameter of this program In addition, the calculations may be performed for a single sequence (against all the other sequences) or for a range of sequences. The query sequence or sequence range must be provided as fourth, or fourth and fifth parameters, respectively
USAGE: ap_PairwiseSequenceIdentityProtocol input.fasta [n_threads [seqID_cutoff [first [last]] ] ] EXAMPLES: ap_PairwiseSequenceIdentityProtocol small500_95identical.fasta 4 0.25 ap_PairwiseSequenceIdentityProtocol small500_95identical.fasta 4 0.25 0 10