}
/**
+ * Compute a globally optimal needleman and wunsch alignment between two
+ * sequences
+ *
+ * @param s1
+ * @param s2
+ * @param type
+ * AlignSeq.DNA or AlignSeq.PEP
+ */
+ public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2,
+ String type)
+ {
+ AlignSeq as = new AlignSeq(s1, s2, type);
+
+ as.calcScoreMatrix();
+ as.traceAlignment();
+ return as;
+ }
+
+
* compute the PID vector used by the redundancy filter.
*
* @param originalSequences