+ this(s, false);
+ }
+
+ /**
+ * Creates a new PCA object.
+ * By default, uses blosum62 matrix to generate sequence similarity matrices
+ * @param s
+ * Set of sequences to perform PCA on
+ * @param nucleotides if true, uses standard DNA/RNA matrix for sequence similarity calculation.
+ */
+ public PCA(String[] s, boolean nucleotides)
+ {