+#define PREPARE_BF_F84\
+ A = (BF[0]*BF[2])/(BF[0] + BF[2]) + (BF[1]*BF[3])/(BF[1] + BF[3]);\
+ B = BF[0]*BF[2] + BF[1]*BF[3];\
+ C = (BF[0] + BF[2])*(BF[1] + BF[3]);
+
+#define COMPUTE_DIST_F84\
+ P = ((double) Ns/L);\
+ Q = ((double) (Nd - Ns)/L);\
+ d[target] = -2*A*log(1 - P/(2*A) - (A - B)*Q/(2*A*C)) + 2*(A - B - C)*log(1 - Q/(2*C));\
+ if (*variance) {\
+ t1 = A*C;\
+ t2 = C*P/2;\
+ t3 = (A - B)*Q/2;\
+ a = t1/(t1 - t2 - t3);\
+ b = A*(A - B)/(t1 - t2 - t3) - (A - B - C)/(C - Q/2);\
+ var[target] = (a*a*P + b*b*Q - pow(a*P + b*Q, 2))/2;\
+ }
+
+void distDNA_F84(unsigned char *x, int *n, int *s, double *d,
+ double *BF, int *variance, double *var)
+{
+ int i1, i2, Nd, Ns, L, target, s1, s2;
+ double P, Q, A, B, C, a, b, t1, t2, t3;
+
+ PREPARE_BF_F84
+ L = *s;
+
+ target = 0;
+ for (i1 = 1; i1 < *n; i1++) {
+ for (i2 = i1 + 1; i2 <= *n; i2++) {
+ Nd = Ns = 0;
+ for (s1 = i1 - 1, s2 = i2 - 1; s1 < i1 + *n*(*s - 1); s1+= *n, s2 += *n) {
+ COUNT_TS_TV
+ }
+ COMPUTE_DIST_F84
+ target++;
+ }
+ }
+}
+
+void distDNA_F84_pairdel(unsigned char *x, int *n, int *s, double *d,
+ double *BF, int *variance, double *var)
+{
+ int i1, i2, Nd, Ns, L, target, s1, s2;
+ double P, Q, A, B, C, a, b, t1, t2, t3;
+
+ PREPARE_BF_F84
+
+ target = 0;
+ for (i1 = 1; i1 < *n; i1++) {
+ for (i2 = i1 + 1; i2 <= *n; i2++) {
+ Nd = Ns = L = 0;
+ for (s1 = i1 - 1, s2 = i2 - 1; s1 < i1 + *n*(*s - 1); s1+= *n, s2 += *n) {
+ CHECK_PAIRWISE_DELETION
+ COUNT_TS_TV
+ }
+ COMPUTE_DIST_F84
+ target++;
+ }
+ }
+}