--- /dev/null
+/////////////////////////////////////////////////////////////////
+// Defaults.h
+//
+// Default constants for use in PROBCONS. The emission
+// probabilities were computed using the program used to build
+// the BLOSUM62 matrix from the BLOCKS 5.0 dataset. Transition
+// parameters were obtained via unsupervised EM training on the
+// BALIBASE 2.0 benchmark alignment database.
+/////////////////////////////////////////////////////////////////
+
+#ifndef DEFAULTS_H
+#define DEFAULTS_H
+
+#include <string>
+
+using namespace std;
+
+float initDistrib1Default[] = { 0.9588437676f, 0.0205782652f, 0.0205782652f };
+float gapOpen1Default[] = { 0.0190259293f, 0.0190259293f };
+float gapExtend1Default[] = { 0.3269913495f, 0.3269913495f };
+
+float initDistrib2Default[] = { 0.9615409374f, 0.0000004538f, 0.0000004538f, 0.0192291681f, 0.0192291681f };
+float gapOpen2Default[] = { 0.0082473317f, 0.0082473317f, 0.0107844425f, 0.0107844425f };
+float gapExtend2Default[] = { 0.3210460842f, 0.3210460842f, 0.3298229277f, 0.3298229277f };
+
+string alphabetDefault = "ACGUTN";
+
+//float emitSingleDefault[6] = {
+// 0.2174750715, 0.2573366761, 0.3005372882, 0.2233072966, 0.2233072966, 0.0004049665
+//};
+
+float emitSingleDefault[6] = {
+ 0.2270790040f, 0.2422080040f, 0.2839320004f, 0.2464679927f, 0.2464679927f, 0.0003124650f
+};
+
+/* ACGUTN */
+
+float emitPairsDefault[6][6] = {
+ { 0.1487240046f, 0.0184142999f, 0.0361397006f, 0.0238473993f, 0.0238473993f, 0.0000375308f },
+ { 0.0184142999f, 0.1583919972f, 0.0275536999f, 0.0389291011f, 0.0389291011f, 0.0000815823f },
+ { 0.0361397006f, 0.0275536999f, 0.1979320049f, 0.0244289003f, 0.0244289003f, 0.0000824765f },
+ { 0.0238473993f, 0.0389291011f, 0.0244289003f, 0.1557479948f, 0.1557479948f, 0.0000743985f },
+ { 0.0238473993f, 0.0389291011f, 0.0244289003f, 0.1557479948f, 0.1557479948f, 0.0000743985f },
+ { 0.0000375308f, 0.0000815823f, 0.0000824765f, 0.0000743985f, 0.0000743985f, 0.0000263252f }
+};
+
+ /*
+float emitPairsDefault[6][6] = {
+ {0.1731323451, 0.0378843173, 0.0656677559, 0.0450690985, 0.0450690985, 0.0000215275},
+ {0.0378843173, 0.1611578614, 0.0492933467, 0.0651549697, 0.0651549697, 0.0000362353},
+ {0.0656677559, 0.0492933467, 0.1937607974, 0.0464556068, 0.0464556068, 0.0000293904},
+ {0.0450690985, 0.0651549697, 0.0464556068, 0.1622997671, 0.1622997671, 0.0000352637},
+ {0.0450690985, 0.0651549697, 0.0464556068, 0.1622997671, 0.1622997671, 0.0000352637},
+ {0.0000215275, 0.0000362353, 0.0000293904, 0.0000352637, 0.0000352637, 0.0000000000}
+};
+ */
+#endif