ap_SequenceWeightingProtocol reads a set of protein sequences and computes a real weight for each of those sequences.
If the FASTA file is the input, every pair of sequences will be aligned and sequence identity values will be evaluated based on these alignments. If .aln is the input (i.e. ClustalO MSA file format), it is assumed the sequences are already aligned and sequence identity values will be computed based on the MSA.
Sequence identity values will be transformed into real weights. These weights may be further used e.g. in sequence profile construction
USAGE: ap_SequenceWeightingProtocol input.fasta ap_SequenceWeightingProtocol input.aln