JSAV is a JavaScript program to display and sort a sequence alignment. The sorting method chooses a representative sequence (one which is most similar to all the other sequences) placing that first in the list. To add to the sorted list, it iteratively chooses the sequences that are most similar to the last one in the list and, of those chooses the sequence most similar to the representative sequence.
Sequences are:
Input to the JavaScript is simply an array of sequences in the form:
sequences[0] = { id :"id1b1.L", sequence :"SASSSVNYMYACREFGHIKLMNPTRSTVWY"};
and the display and sorter is created with
printJSAV('sequenceDisplay', sequences, options);
sequenceDisplay - div in which to display the viewer
sequences - array of sequence objects
options - an object describing options