diff --git a/src/core_derivatives.c b/src/core_derivatives.c
index 885b952..ee8fe62 100644
--- a/src/core_derivatives.c
+++ b/src/core_derivatives.c
@@ -702,7 +702,7 @@ PLL_EXPORT int pll_core_likelihood_derivatives(unsigned int states,
                                                unsigned int parent_sites,
                                                unsigned int child_ids,
                                                const int * invariant,
-                                               const unsigned int * pattern_weights,
+                                               const double * pattern_weights,
                                                double branch_length,
                                                const double * prop_invar,
                                                double * const * freqs,
@@ -897,7 +897,7 @@ PLL_EXPORT int pll_core_likelihood_derivatives(unsigned int states,
         case PLL_ATTRIB_AB_LEWIS:
         {
           // TODO: pattern_weight_sum should be stored somewhere!
-          unsigned int pattern_weight_sum = 0;
+          double pattern_weight_sum = 0;
           for (n = 0; n < ef_sites; ++n)
             pattern_weight_sum += pattern_weights[n];
 
diff --git a/src/core_derivatives_avx.c b/src/core_derivatives_avx.c
index 804a66e..482a52b 100644
--- a/src/core_derivatives_avx.c
+++ b/src/core_derivatives_avx.c
@@ -1616,7 +1616,7 @@ PLL_EXPORT int pll_core_likelihood_derivatives_avx(unsigned int states,
                                                    unsigned int states_padded,
                                                    unsigned int rate_cats,
                                                    unsigned int ef_sites,
-                                                   const unsigned int * pattern_weights,
+                                                   const double * pattern_weights,
                                                    const double * rate_weights,
                                                    const int * invariant,
                                                    const double * prop_invar,
@@ -1840,8 +1840,10 @@ PLL_EXPORT int pll_core_likelihood_derivatives_avx(unsigned int states,
                                        _mm256_mul_pd(v_term2, v_recip0));
 
       /* assumption: no zero weights */
-      if ((pattern_weights[n-3] | pattern_weights[n-2] |
-           pattern_weights[n-1] | pattern_weights[n]) == 1)
+      //if ((pattern_weights[n-3] | pattern_weights[n-2] |
+      //     pattern_weights[n-1] | pattern_weights[n]) == 1)
+      if (pattern_weights[n-3] == 1.0 && pattern_weights[n-2] == 1.0 &&
+          pattern_weights[n-1] == 1.0 && pattern_weights[n] == 1.0)
       {
         /* all 4 weights are 1 -> no multiplication needed */
         v_df = _mm256_sub_pd (v_df, v_deriv1);
@@ -1849,9 +1851,9 @@ PLL_EXPORT int pll_core_likelihood_derivatives_avx(unsigned int states,
       }
       else
       {
+
         __m256d v_patw = _mm256_setr_pd(pattern_weights[n-3], pattern_weights[n-2],
                                         pattern_weights[n-1], pattern_weights[n]);
-
         v_df = _mm256_sub_pd (v_df, _mm256_mul_pd(v_deriv1, v_patw));
         v_ddf = _mm256_add_pd (v_ddf, _mm256_mul_pd(v_deriv2, v_patw));
       }
diff --git a/src/core_derivatives_avx2.c b/src/core_derivatives_avx2.c
index 5c58d74..ad44695 100644
--- a/src/core_derivatives_avx2.c
+++ b/src/core_derivatives_avx2.c
@@ -1540,7 +1540,7 @@ int pll_core_likelihood_derivatives_avx2(unsigned int states,
                                          unsigned int states_padded,
                                          unsigned int rate_cats,
                                          unsigned int ef_sites,
-                                         const unsigned int * pattern_weights,
+                                         const double * pattern_weights,
                                          const double * rate_weights,
                                          const int * invariant,
                                          const double * prop_invar,
@@ -1764,8 +1764,10 @@ int pll_core_likelihood_derivatives_avx2(unsigned int states,
                                        _mm256_mul_pd(v_term2, v_recip0));
 
       /* assumption: no zero weights */
-      if ((pattern_weights[n-3] | pattern_weights[n-2] |
-           pattern_weights[n-1] | pattern_weights[n]) == 1)
+      //if ((pattern_weights[n-3] | pattern_weights[n-2] |
+      //     pattern_weights[n-1] | pattern_weights[n]) == 1)
+      if (pattern_weights[n-3] == 1.0 && pattern_weights[n-2] == 1.0 &&
+          pattern_weights[n-1] == 1.0 && pattern_weights[n] == 1.0)
       {
         /* all 4 weights are 1 -> no multiplication needed */
         v_df = _mm256_sub_pd (v_df, v_deriv1);
diff --git a/src/core_likelihood.c b/src/core_likelihood.c
index b7cbd4e..86da0a1 100644
--- a/src/core_likelihood.c
+++ b/src/core_likelihood.c
@@ -29,7 +29,7 @@ PLL_EXPORT double pll_core_root_loglikelihood(unsigned int states,
                                               const unsigned int * scaler,
                                               double * const * frequencies,
                                               const double * rate_weights,
-                                              const unsigned int * pattern_weights,
+                                              const double * pattern_weights,
                                               const double * invar_proportion,
                                               const int * invar_indices,
                                               const unsigned int * freqs_indices,
@@ -216,7 +216,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_repeats_generic(unsigned int state
                                                               const unsigned int * scaler,
                                                               double * const * frequencies,
                                                               const double * rate_weights,
-                                                              const unsigned int * pattern_weights,
+                                                              const double * pattern_weights,
                                                               const double * invar_proportion,
                                                               const int * invar_indices,
                                                               const unsigned int * freqs_indices,
@@ -292,7 +292,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_repeats(unsigned int states,
                                                       const unsigned int * scaler,
                                                       double * const * frequencies,
                                                       const double * rate_weights,
-                                                      const unsigned int * pattern_weights,
+                                                      const double * pattern_weights,
                                                       const double * invar_proportion,
                                                       const int * invar_indices,
                                                       const unsigned int * freqs_indices,
@@ -307,7 +307,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_repeats(unsigned int states,
                                      const unsigned int * scaler,
                                      double * const * frequencies,
                                      const double * rate_weights,
-                                     const unsigned int * pattern_weights,
+                                     const double * pattern_weights,
                                      const double * invar_proportion,
                                      const int * invar_indices,
                                      const unsigned int * freqs_indices,
@@ -357,7 +357,7 @@ double pll_core_edge_loglikelihood_ti_4x4(unsigned int sites,
                                           const double * pmatrix,
                                           double * const * frequencies,
                                           const double * rate_weights,
-                                          const unsigned int * pattern_weights,
+                                          const double * pattern_weights,
                                           const double * invar_proportion,
                                           const int * invar_indices,
                                           const unsigned int * freqs_indices,
@@ -589,7 +589,7 @@ double pll_core_edge_loglikelihood_ti(unsigned int states,
                                       const double * pmatrix,
                                       double * const * frequencies,
                                       const double * rate_weights,
-                                      const unsigned int * pattern_weights,
+                                      const double * pattern_weights,
                                       const double * invar_proportion,
                                       const int * invar_indices,
                                       const unsigned int * freqs_indices,
@@ -932,7 +932,7 @@ double pll_core_edge_loglikelihood_repeats(unsigned int states,
                                            const double * pmatrix,
                                            double ** frequencies,
                                            const double * rate_weights,
-                                           const unsigned int * pattern_weights,
+                                           const double * pattern_weights,
                                            const double * invar_proportion,
                                            const int * invar_indices,
                                            const unsigned int * freqs_indices,
@@ -953,7 +953,7 @@ double pll_core_edge_loglikelihood_repeats(unsigned int states,
                                     const double * pmatrix,
                                     double ** frequencies,
                                     const double * rate_weights,
-                                    const unsigned int * pattern_weights,
+                                    const double * pattern_weights,
                                     const double * invar_proportion,
                                     const int * invar_indices,
                                     const unsigned int * freqs_indices,
@@ -1026,7 +1026,7 @@ double pll_core_edge_loglikelihood_repeats_generic(unsigned int states,
                                                    const double * pmatrix,
                                                    double ** frequencies,
                                                    const double * rate_weights,
-                                                   const unsigned int * pattern_weights,
+                                                   const double * pattern_weights,
                                                    const double * invar_proportion,
                                                    const int * invar_indices,
                                                    const unsigned int * freqs_indices,
@@ -1199,7 +1199,7 @@ double pll_core_edge_loglikelihood_ii(unsigned int states,
                                       const double * pmatrix,
                                       double * const * frequencies,
                                       const double * rate_weights,
-                                      const unsigned int * pattern_weights,
+                                      const double * pattern_weights,
                                       const double * invar_proportion,
                                       const int * invar_indices,
                                       const unsigned int * freqs_indices,
diff --git a/src/core_likelihood_avx.c b/src/core_likelihood_avx.c
index 4e80c7a..317757f 100644
--- a/src/core_likelihood_avx.c
+++ b/src/core_likelihood_avx.c
@@ -29,7 +29,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_avx(unsigned int states,
                                                   const unsigned int * scaler,
                                                   double * const * frequencies,
                                                   const double * rate_weights,
-                                                  const unsigned int * pattern_weights,
+                                                  const double * pattern_weights,
                                                   const double * invar_proportion,
                                                   const int * invar_indices,
                                                   const unsigned int * freqs_indices,
@@ -118,7 +118,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_repeats_avx(unsigned int states,
                                                           const unsigned int * scaler,
                                                           double * const * frequencies,
                                                           const double * rate_weights,
-                                                          const unsigned int * pattern_weights,
+                                                          const double * pattern_weights,
                                                           const double * invar_proportion,
                                                           const int * invar_indices,
                                                           const unsigned int * freqs_indices,
@@ -209,7 +209,7 @@ double pll_core_root_loglikelihood_4x4_avx(unsigned int sites,
                                            const unsigned int * scaler,
                                            double * const * frequencies,
                                            const double * rate_weights,
-                                           const unsigned int * pattern_weights,
+                                           const double * pattern_weights,
                                            const double * invar_proportion,
                                            const int * invar_indices,
                                            const unsigned int * freqs_indices,
@@ -291,7 +291,7 @@ double pll_core_edge_loglikelihood_ti_4x4_avx(unsigned int sites,
                                               const double * pmatrix,
                                               double * const * frequencies,
                                               const double * rate_weights,
-                                              const unsigned int * pattern_weights,
+                                              const double * pattern_weights,
                                               const double * invar_proportion,
                                               const int * invar_indices,
                                               const unsigned int * freqs_indices,
@@ -537,7 +537,7 @@ double pll_core_edge_loglikelihood_ti_20x20_avx(unsigned int sites,
                                                 const double * pmatrix,
                                                 double * const * frequencies,
                                                 const double * rate_weights,
-                                                const unsigned int * pattern_weights,
+                                                const double * pattern_weights,
                                                 const double * invar_proportion,
                                                 const int * invar_indices,
                                                 const unsigned int * freqs_indices,
@@ -782,7 +782,7 @@ double pll_core_edge_loglikelihood_ti_avx(unsigned int states,
                                           const double * pmatrix,
                                           double * const * frequencies,
                                           const double * rate_weights,
-                                          const unsigned int * pattern_weights,
+                                          const double * pattern_weights,
                                           const double * invar_proportion,
                                           const int * invar_indices,
                                           const unsigned int * freqs_indices,
@@ -1031,7 +1031,7 @@ double pll_core_edge_loglikelihood_repeats_generic_avx(unsigned int states,
                                                        const double * pmatrix,
                                                        double ** frequencies,
                                                        const double * rate_weights,
-                                                       const unsigned int * pattern_weights,
+                                                       const double * pattern_weights,
                                                        const double * invar_proportion,
                                                        const int * invar_indices,
                                                        const unsigned int * freqs_indices,
@@ -1278,7 +1278,7 @@ double pll_core_edge_loglikelihood_ii_avx(unsigned int states,
                                           const double * pmatrix,
                                           double * const * frequencies,
                                           const double * rate_weights,
-                                          const unsigned int * pattern_weights,
+                                          const double * pattern_weights,
                                           const double * invar_proportion,
                                           const int * invar_indices,
                                           const unsigned int * freqs_indices,
@@ -1519,7 +1519,7 @@ double pll_core_edge_loglikelihood_ii_4x4_avx(unsigned int sites,
                                               const double * pmatrix,
                                               double * const * frequencies,
                                               const double * rate_weights,
-                                              const unsigned int * pattern_weights,
+                                              const double * pattern_weights,
                                               const double * invar_proportion,
                                               const int * invar_indices,
                                               const unsigned int * freqs_indices,
@@ -1737,7 +1737,7 @@ double pll_core_edge_loglikelihood_repeats_4x4_avx(unsigned int states,
                                                    const double * pmatrix,
                                                    double ** frequencies,
                                                    const double * rate_weights,
-                                                   const unsigned int * pattern_weights,
+                                                   const double * pattern_weights,
                                                    const double * invar_proportion,
                                                    const int * invar_indices,
                                                    const unsigned int * freqs_indices,
@@ -1957,7 +1957,7 @@ double pll_core_edge_loglikelihood_repeatsbclv_4x4_avx(unsigned int states,
                                                        const double * pmatrix,
                                                        double ** frequencies,
                                                        const double * rate_weights,
-                                                       const unsigned int * pattern_weights,
+                                                       const double * pattern_weights,
                                                        const double * invar_proportion,
                                                        const int * invar_indices,
                                                        const unsigned int * freqs_indices,
diff --git a/src/core_likelihood_avx2.c b/src/core_likelihood_avx2.c
index 8c577d8..9dfa092 100644
--- a/src/core_likelihood_avx2.c
+++ b/src/core_likelihood_avx2.c
@@ -29,7 +29,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_avx2(unsigned int states,
                                                    const unsigned int * scaler,
                                                    double * const * frequencies,
                                                    const double * rate_weights,
-                                                   const unsigned int * pattern_weights,
+                                                   const double * pattern_weights,
                                                    const double * invar_proportion,
                                                    const int * invar_indices,
                                                    const unsigned int * freqs_indices,
@@ -116,7 +116,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_repeats_avx2(unsigned int states,
                                                   const unsigned int * scaler,
                                                   double * const * frequencies,
                                                   const double * rate_weights,
-                                                  const unsigned int * pattern_weights,
+                                                  const double * pattern_weights,
                                                   const double * invar_proportion,
                                                   const int * invar_indices,
                                                   const unsigned int * freqs_indices,
@@ -209,7 +209,7 @@ double pll_core_edge_loglikelihood_ti_20x20_avx2(unsigned int sites,
                                                  const double * pmatrix,
                                                  double * const * frequencies,
                                                  const double * rate_weights,
-                                                 const unsigned int * pattern_weights,
+                                                 const double * pattern_weights,
                                                  const double * invar_proportion,
                                                  const int * invar_indices,
                                                  const unsigned int * freqs_indices,
@@ -456,7 +456,7 @@ double pll_core_edge_loglikelihood_ii_avx2(unsigned int states,
                                            const double * pmatrix,
                                            double * const * frequencies,
                                            const double * rate_weights,
-                                           const unsigned int * pattern_weights,
+                                           const double * pattern_weights,
                                            const double * invar_proportion,
                                            const int * invar_indices,
                                            const unsigned int * freqs_indices,
@@ -694,7 +694,7 @@ double pll_core_edge_loglikelihood_repeats_generic_avx2(unsigned int states,
                                                         const double * pmatrix,
                                                         double ** frequencies,
                                                         const double * rate_weights,
-                                                        const unsigned int * pattern_weights,
+                                                        const double * pattern_weights,
                                                         const double * invar_proportion,
                                                         const int * invar_indices,
                                                         const unsigned int * freqs_indices,
diff --git a/src/core_likelihood_sse.c b/src/core_likelihood_sse.c
index 7bfc559..279130f 100644
--- a/src/core_likelihood_sse.c
+++ b/src/core_likelihood_sse.c
@@ -29,7 +29,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_sse(unsigned int states,
                                                   const unsigned int * scaler,
                                                   double * const * frequencies,
                                                   const double * rate_weights,
-                                                  const unsigned int * pattern_weights,
+                                                  const double * pattern_weights,
                                                   const double * invar_proportion,
                                                   const int * invar_indices,
                                                   const unsigned int * freqs_indices,
@@ -115,7 +115,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_repeats_sse(unsigned int states,
                                                           const unsigned int * scaler,
                                                           double * const * frequencies,
                                                           const double * rate_weights,
-                                                          const unsigned int * pattern_weights,
+                                                          const double * pattern_weights,
                                                           const double * invar_proportion,
                                                           const int * invar_indices,
                                                           const unsigned int * freqs_indices,
@@ -202,7 +202,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_4x4_sse(unsigned int sites,
                                                       const unsigned int * scaler,
                                                       double * const * frequencies,
                                                       const double * rate_weights,
-                                                      const unsigned int * pattern_weights,
+                                                      const double * pattern_weights,
                                                       const double * invar_proportion,
                                                       const int * invar_indices,
                                                       const unsigned int * freqs_indices,
@@ -287,7 +287,7 @@ double pll_core_edge_loglikelihood_ti_sse(unsigned int states,
                                           const double * pmatrix,
                                           double * const * frequencies,
                                           const double * rate_weights,
-                                          const unsigned int * pattern_weights,
+                                          const double * pattern_weights,
                                           const double * invar_proportion,
                                           const int * invar_indices,
                                           const unsigned int * freqs_indices,
@@ -509,7 +509,7 @@ double pll_core_edge_loglikelihood_ii_sse(unsigned int states,
                                           const double * pmatrix,
                                           double * const * frequencies,
                                           const double * rate_weights,
-                                          const unsigned int * pattern_weights,
+                                          const double * pattern_weights,
                                           const double * invar_proportion,
                                           const int * invar_indices,
                                           const unsigned int * freqs_indices,
@@ -723,7 +723,7 @@ double pll_core_edge_loglikelihood_repeats_generic_sse(unsigned int states,
                                                        const double * pmatrix,
                                                        double ** frequencies,
                                                        const double * rate_weights,
-                                                       const unsigned int * pattern_weights,
+                                                       const double * pattern_weights,
                                                        const double * invar_proportion,
                                                        const int * invar_indices,
                                                        const unsigned int * freqs_indices,
@@ -941,7 +941,7 @@ double pll_core_edge_loglikelihood_ii_4x4_sse(unsigned int sites,
                                               const double * pmatrix,
                                               double * const * frequencies,
                                               const double * rate_weights,
-                                              const unsigned int * pattern_weights,
+                                              const double * pattern_weights,
                                               const double * invar_proportion,
                                               const int * invar_indices,
                                               const unsigned int * freqs_indices,
@@ -1182,7 +1182,7 @@ double pll_core_edge_loglikelihood_ti_4x4_sse(unsigned int sites,
                                               const double * pmatrix,
                                               double * const * frequencies,
                                               const double * rate_weights,
-                                              const unsigned int * pattern_weights,
+                                              const double * pattern_weights,
                                               const double * invar_proportion,
                                               const int * invar_indices,
                                               const unsigned int * freqs_indices,
diff --git a/src/fast_parsimony.c b/src/fast_parsimony.c
index 3b3e5f4..e0133eb 100644
--- a/src/fast_parsimony.c
+++ b/src/fast_parsimony.c
@@ -242,7 +242,7 @@ static int fill_parsimony_vectors(const pll_partition_t * partition,
   /* compute total number of bits required */
   for (i=0; i<parsimony->sites; ++i)
     if (parsimony->informative[i])
-      bitcount += partition->pattern_weights[i];
+      bitcount += (int)partition->pattern_weights[i];
 
   /* number of 32-bit bit-vectors required */
   bitvectors = (bitcount / PLL_BITVECTOR_SIZE) +
@@ -300,7 +300,7 @@ static int fill_parsimony_vectors(const pll_partition_t * partition,
       {
         /* TODO: check for tip map */
         unsigned int m;
-        for (m = 0; m < partition->pattern_weights[j]; ++m)
+        for (m = 0; m < (unsigned int)partition->pattern_weights[j]; ++m)
         {
           if (parsimony->attributes & PLL_ATTRIB_PATTERN_TIP)
           {
diff --git a/src/likelihood.c b/src/likelihood.c
index b069f03..76bf6c8 100644
--- a/src/likelihood.c
+++ b/src/likelihood.c
@@ -62,7 +62,7 @@ static double root_loglikelihood_asc_bias(pll_partition_t * partition,
    unsigned int states = partition->states;
    unsigned int states_padded = partition->states_padded;
    unsigned int scale_factors;
-   unsigned int * pattern_weights = partition->pattern_weights;
+   double * pattern_weights = partition->pattern_weights;
    double * rate_weights = partition->rate_weights;
 
    double logl_correction = 0;
@@ -205,7 +205,7 @@ static double edge_loglikelihood_asc_bias_ti(pll_partition_t * partition,
   unsigned int states = partition->states;
   unsigned int states_padded = partition->states_padded;
   unsigned int scale_factors;
-  unsigned int * pattern_weights = partition->pattern_weights;
+  double * pattern_weights = partition->pattern_weights;
   double * rate_weights = partition->rate_weights;
 
   double logl_correction = 0;
@@ -359,7 +359,7 @@ static double edge_loglikelihood_asc_bias_ii(pll_partition_t * partition,
   unsigned int states = partition->states;
   unsigned int states_padded = partition->states_padded;
   unsigned int scale_factors;
-  unsigned int * pattern_weights = partition->pattern_weights;
+  double * pattern_weights = partition->pattern_weights;
   double * rate_weights = partition->rate_weights;
 
   /* point clv, clvc, scalers and pattern weights to state sites */
diff --git a/src/pll.c b/src/pll.c
index 3b6be68..c9d3f44 100644
--- a/src/pll.c
+++ b/src/pll.c
@@ -808,8 +808,8 @@ PLL_EXPORT pll_partition_t * pll_partition_create(unsigned int tips,
   }
 
   /* site weights */
-  partition->pattern_weights = (unsigned int *)malloc(sites_alloc *
-                                                      sizeof(unsigned int));
+  partition->pattern_weights = (double *)malloc(sites_alloc *
+                                                      sizeof(double));
   if (!partition->pattern_weights)
   {
     dealloc_partition_data(partition);
@@ -1110,12 +1110,12 @@ PLL_EXPORT int pll_set_tip_clv(pll_partition_t * partition,
 }
 
 PLL_EXPORT void pll_set_pattern_weights(pll_partition_t * partition,
-                                        const unsigned int * pattern_weights)
+                                        const double * pattern_weights)
 {
   unsigned int i;
   memcpy(partition->pattern_weights,
          pattern_weights,
-         sizeof(unsigned int)*partition->sites);
+         sizeof(double)*partition->sites);
 
   /* recompute the sum of weights */
   partition->pattern_weight_sum = 0;
@@ -1172,12 +1172,12 @@ PLL_EXPORT int pll_set_asc_bias_type(pll_partition_t * partition,
 }
 
 PLL_EXPORT void pll_set_asc_state_weights(pll_partition_t * partition,
-                                          const unsigned int * state_weights)
+                                          const double * state_weights)
 {
   assert(partition->asc_bias_alloc);
   memcpy(partition->pattern_weights + partition->sites,
          state_weights,
-         sizeof(unsigned int)*partition->states);
+         sizeof(double)*partition->states);
 }
 
 PLL_EXPORT void pll_fill_parent_scaler(unsigned int scaler_size,
diff --git a/src/pll.h b/src/pll.h
index 8a4e361..ffdc3bb 100644
--- a/src/pll.h
+++ b/src/pll.h
@@ -234,7 +234,7 @@ typedef struct pll_partition
   unsigned int nodes; // tips + clv_buffer
   unsigned int states;
   unsigned int sites;
-  unsigned int pattern_weight_sum;
+  double pattern_weight_sum;
   unsigned int rate_matrices;
   unsigned int prob_matrices;
   unsigned int rate_cats;
@@ -254,7 +254,7 @@ typedef struct pll_partition
   double ** frequencies;
   double * prop_invar;
   int * invariant;
-  unsigned int * pattern_weights;
+  double * pattern_weights;
 
   int * eigen_decomp_valid;
   double ** eigenvecs;
@@ -626,13 +626,13 @@ PLL_EXPORT int pll_set_tip_clv(pll_partition_t * partition,
                                int padding);
 
 PLL_EXPORT void pll_set_pattern_weights(pll_partition_t * partition,
-                                        const unsigned int * pattern_weights);
+                                        const double * pattern_weights);
 
 PLL_EXPORT int pll_set_asc_bias_type(pll_partition_t * partition,
                                      int asc_bias_type);
 
 PLL_EXPORT void pll_set_asc_state_weights(pll_partition_t * partition,
-                                          const unsigned int * state_weights);
+                                          const double * state_weights);
 
 /* functions in list.c */
 
@@ -1229,7 +1229,7 @@ PLL_EXPORT int pll_core_likelihood_derivatives(unsigned int states,
                                                unsigned int parent_ids,
                                                unsigned int child_ids,
                                                const int * invariant,
-                                               const unsigned int * pattern_weights,
+                                               const double * pattern_weights,
                                                double branch_length,
                                                const double * prop_invar,
                                                double * const * freqs,
@@ -1270,7 +1270,7 @@ PLL_EXPORT double pll_core_edge_loglikelihood_ii(unsigned int states,
                                                  const double * pmatrix,
                                                  double * const * frequencies,
                                                  const double * rate_weights,
-                                                 const unsigned int * pattern_weights,
+                                                 const double * pattern_weights,
                                                  const double * invar_proportion,
                                                  const int * invar_indices,
                                                  const unsigned int * freqs_indices,
@@ -1288,7 +1288,7 @@ PLL_EXPORT double pll_core_edge_loglikelihood_ti(unsigned int states,
                                                  const double * pmatrix,
                                                  double * const * frequencies,
                                                  const double * rate_weights,
-                                                 const unsigned int * pattern_weights,
+                                                 const double * pattern_weights,
                                                  const double * invar_proportion,
                                                  const int * invar_indices,
                                                  const unsigned int * freqs_indices,
@@ -1303,7 +1303,7 @@ PLL_EXPORT double pll_core_edge_loglikelihood_ti_4x4(unsigned int sites,
                                                      const double * pmatrix,
                                                      double * const * frequencies,
                                                      const double * rate_weights,
-                                                     const unsigned int * pattern_weights,
+                                                     const double * pattern_weights,
                                                      const double * invar_proportion,
                                                      const int * invar_indices,
                                                      const unsigned int * freqs_indices,
@@ -1318,7 +1318,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_repeats(unsigned int states,
                                                       const unsigned int * scaler,
                                                       double * const * frequencies,
                                                       const double * rate_weights,
-                                                      const unsigned int * pattern_weights,
+                                                      const double * pattern_weights,
                                                       const double * invar_proportion,
                                                       const int * invar_indices,
                                                       const unsigned int * freqs_indices,
@@ -1336,7 +1336,7 @@ PLL_EXPORT double pll_core_edge_loglikelihood_repeats(unsigned int states,
                                                       const double * pmatrix,
                                                       double ** frequencies,
                                                       const double * rate_weights,
-                                                      const unsigned int * pattern_weights,
+                                                      const double * pattern_weights,
                                                       const double * invar_proportion,
                                                       const int * invar_indices,
                                                       const unsigned int * freqs_indices,
@@ -1357,7 +1357,7 @@ PLL_EXPORT double pll_core_edge_loglikelihood_repeats_generic(unsigned int state
                                       const double * pmatrix,
                                       double ** frequencies,
                                       const double * rate_weights,
-                                      const unsigned int * pattern_weights,
+                                      const double * pattern_weights,
                                       const double * invar_proportion,
                                       const int * invar_indices,
                                       const unsigned int * freqs_indices,
@@ -1374,7 +1374,7 @@ PLL_EXPORT double pll_core_root_loglikelihood(unsigned int states,
                                               const unsigned int * scaler,
                                               double * const * frequencies,
                                               const double * rate_weights,
-                                              const unsigned int * pattern_weights,
+                                              const double * pattern_weights,
                                               const double * invar_proportion,
                                               const int * invar_indices,
                                               const unsigned int * freqs_indices,
@@ -1820,7 +1820,7 @@ PLL_EXPORT int pll_core_likelihood_derivatives_avx(unsigned int states,
                                                    unsigned int states_padded,
                                                    unsigned int rate_cats,
                                                    unsigned int ef_sites,
-                                                   const unsigned int * pattern_weights,
+                                                   const double * pattern_weights,
                                                    const double * rate_weights,
                                                    const int * invariant,
                                                    const double * prop_invar,
@@ -1919,7 +1919,7 @@ int pll_core_likelihood_derivatives_avx2(unsigned int states,
                                          unsigned int states_padded,
                                          unsigned int rate_cats,
                                          unsigned int ef_sites,
-                                         const unsigned int * pattern_weights,
+                                         const double * pattern_weights,
                                          const double * rate_weights,
                                          const int * invariant,
                                          const double * prop_invar,
@@ -1962,7 +1962,7 @@ double pll_core_edge_loglikelihood_ii_sse(unsigned int states,
                                           const double * pmatrix,
                                           double * const * frequencies,
                                           const double * rate_weights,
-                                          const unsigned int * pattern_weights,
+                                          const double * pattern_weights,
                                           const double * invar_proportion,
                                           const int * invar_indices,
                                           const unsigned int * freqs_indices,
@@ -1979,7 +1979,7 @@ double pll_core_edge_loglikelihood_ii_4x4_sse(unsigned int sites,
                                               const double * pmatrix,
                                               double * const * frequencies,
                                               const double * rate_weights,
-                                              const unsigned int * pattern_weights,
+                                              const double * pattern_weights,
                                               const double * invar_proportion,
                                               const int * invar_indices,
                                               const unsigned int * freqs_indices,
@@ -1997,7 +1997,7 @@ double pll_core_edge_loglikelihood_ti_sse(unsigned int states,
                                           const double * pmatrix,
                                           double * const * frequencies,
                                           const double * rate_weights,
-                                          const unsigned int * pattern_weights,
+                                          const double * pattern_weights,
                                           const double * invar_proportion,
                                           const int * invar_indices,
                                           const unsigned int * freqs_indices,
@@ -2013,7 +2013,7 @@ double pll_core_edge_loglikelihood_ti_4x4_sse(unsigned int sites,
                                               const double * pmatrix,
                                               double * const * frequencies,
                                               const double * rate_weights,
-                                              const unsigned int * pattern_weights,
+                                              const double * pattern_weights,
                                               const double * invar_proportion,
                                               const int * invar_indices,
                                               const unsigned int * freqs_indices,
@@ -2026,7 +2026,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_4x4_sse(unsigned int sites,
                                                       const unsigned int * scaler,
                                                       double * const * frequencies,
                                                       const double * rate_weights,
-                                                      const unsigned int * pattern_weights,
+                                                      const double * pattern_weights,
                                                       const double * invar_proportion,
                                                       const int * invar_indices,
                                                       const unsigned int * freqs_indices,
@@ -2039,7 +2039,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_sse(unsigned int states,
                                                   const unsigned int * scaler,
                                                   double * const * frequencies,
                                                   const double * rate_weights,
-                                                  const unsigned int * pattern_weights,
+                                                  const double * pattern_weights,
                                                   const double * invar_proportion,
                                                   const int * invar_indices,
                                                   const unsigned int * freqs_indices,
@@ -2053,7 +2053,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_repeats_sse(unsigned int states,
                                                           const unsigned int * scaler,
                                                           double * const * frequencies,
                                                           const double * rate_weights,
-                                                          const unsigned int * pattern_weights,
+                                                          const double * pattern_weights,
                                                           const double * invar_proportion,
                                                           const int * invar_indices,
                                                           const unsigned int * freqs_indices,
@@ -2070,7 +2070,7 @@ PLL_EXPORT double pll_core_edge_loglikelihood_repeats_generic_sse(unsigned int s
                                                                   const double * pmatrix,
                                                                   double ** frequencies,
                                                                   const double * rate_weights,
-                                                                  const unsigned int * pattern_weights,
+                                                                  const double * pattern_weights,
                                                                   const double * invar_proportion,
                                                                   const int * invar_indices,
                                                                   const unsigned int * freqs_indices,
@@ -2094,7 +2094,7 @@ PLL_EXPORT double pll_core_edge_loglikelihood_ii_avx(unsigned int states,
                                                      const double * pmatrix,
                                                      double * const * frequencies,
                                                      const double * rate_weights,
-                                                     const unsigned int * pattern_weights,
+                                                     const double * pattern_weights,
                                                      const double * invar_proportion,
                                                      const int * invar_indices,
                                                      const unsigned int * freqs_indices,
@@ -2110,7 +2110,7 @@ PLL_EXPORT double pll_core_edge_loglikelihood_ii_4x4_avx(unsigned int sites,
                                                          const double * pmatrix,
                                                          double * const * frequencies,
                                                          const double * rate_weights,
-                                                         const unsigned int * pattern_weights,
+                                                         const double * pattern_weights,
                                                          const double * invar_proportion,
                                                          const int * invar_indices,
                                                          const unsigned int * freqs_indices,
@@ -2125,7 +2125,7 @@ PLL_EXPORT double pll_core_edge_loglikelihood_ti_4x4_avx(unsigned int sites,
                                                          const double * pmatrix,
                                                          double * const * frequencies,
                                                          const double * rate_weights,
-                                                         const unsigned int * pattern_weights,
+                                                         const double * pattern_weights,
                                                          const double * invar_proportion,
                                                          const int * invar_indices,
                                                          const unsigned int * freqs_indices,
@@ -2142,7 +2142,7 @@ PLL_EXPORT double pll_core_edge_loglikelihood_ti_20x20_avx(unsigned int sites,
                                                            const double * pmatrix,
                                                            double * const * frequencies,
                                                            const double * rate_weights,
-                                                           const unsigned int * pattern_weights,
+                                                           const double * pattern_weights,
                                                            const double * invar_proportion,
                                                            const int * invar_indices,
                                                            const unsigned int * freqs_indices,
@@ -2159,7 +2159,7 @@ PLL_EXPORT double pll_core_edge_loglikelihood_ti_avx(unsigned int states,
                                                      const double * pmatrix,
                                                      double * const * frequencies,
                                                      const double * rate_weights,
-                                                     const unsigned int * pattern_weights,
+                                                     const double * pattern_weights,
                                                      const double * invar_proportion,
                                                      const int * invar_indices,
                                                      const unsigned int * freqs_indices,
@@ -2172,7 +2172,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_4x4_avx(unsigned int sites,
                                                       const unsigned int * scaler,
                                                       double * const * frequencies,
                                                       const double * rate_weights,
-                                                      const unsigned int * pattern_weights,
+                                                      const double * pattern_weights,
                                                       const double * invar_proportion,
                                                       const int * invar_indices,
                                                       const unsigned int * freqs_indices,
@@ -2185,7 +2185,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_avx(unsigned int states,
                                                   const unsigned int * scaler,
                                                   double * const * frequencies,
                                                   const double * rate_weights,
-                                                  const unsigned int * pattern_weights,
+                                                  const double * pattern_weights,
                                                   const double * invar_proportion,
                                                   const int * invar_indices,
                                                   const unsigned int * freqs_indices,
@@ -2199,7 +2199,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_repeats_avx(unsigned int states,
                                                           const unsigned int * scaler,
                                                           double * const * frequencies,
                                                           const double * rate_weights,
-                                                          const unsigned int * pattern_weights,
+                                                          const double * pattern_weights,
                                                           const double * invar_proportion,
                                                           const int * invar_indices,
                                                           const unsigned int * freqs_indices,
@@ -2216,7 +2216,7 @@ PLL_EXPORT double pll_core_edge_loglikelihood_repeats_generic_avx(unsigned int s
                                                                   const double * pmatrix,
                                                                   double ** frequencies,
                                                                   const double * rate_weights,
-                                                                  const unsigned int * pattern_weights,
+                                                                  const double * pattern_weights,
                                                                   const double * invar_proportion,
                                                                   const int * invar_indices,
                                                                   const unsigned int * freqs_indices,
@@ -2237,7 +2237,7 @@ PLL_EXPORT double pll_core_edge_loglikelihood_repeats_4x4_avx(unsigned int state
                                                               const double * pmatrix,
                                                               double ** frequencies,
                                                               const double * rate_weights,
-                                                              const unsigned int * pattern_weights,
+                                                              const double * pattern_weights,
                                                               const double * invar_proportion,
                                                               const int * invar_indices,
                                                               const unsigned int * freqs_indices,
@@ -2258,7 +2258,7 @@ PLL_EXPORT double pll_core_edge_loglikelihood_repeatsbclv_4x4_avx(unsigned int s
                                                                   const double * pmatrix,
                                                                   double ** frequencies,
                                                                   const double * rate_weights,
-                                                                  const unsigned int * pattern_weights,
+                                                                  const double * pattern_weights,
                                                                   const double * invar_proportion,
                                                                   const int * invar_indices,
                                                                   const unsigned int * freqs_indices,
@@ -2281,7 +2281,7 @@ double pll_core_root_loglikelihood_avx2(unsigned int states,
                                         const unsigned int * scaler,
                                         double * const * frequencies,
                                         const double * rate_weights,
-                                        const unsigned int * pattern_weights,
+                                        const double * pattern_weights,
                                         const double * invar_proportion,
                                         const int * invar_indices,
                                         const unsigned int * freqs_indices,
@@ -2298,7 +2298,7 @@ double pll_core_edge_loglikelihood_ti_20x20_avx2(unsigned int sites,
                                                  const double * pmatrix,
                                                  double * const * frequencies,
                                                  const double * rate_weights,
-                                                 const unsigned int * pattern_weights,
+                                                 const double * pattern_weights,
                                                  const double * invar_proportion,
                                                  const int * invar_indices,
                                                  const unsigned int * freqs_indices,
@@ -2317,7 +2317,7 @@ double pll_core_edge_loglikelihood_ii_avx2(unsigned int states,
                                            const double * pmatrix,
                                            double * const * frequencies,
                                            const double * rate_weights,
-                                           const unsigned int * pattern_weights,
+                                           const double * pattern_weights,
                                            const double * invar_proportion,
                                            const int * invar_indices,
                                            const unsigned int * freqs_indices,
@@ -2333,7 +2333,7 @@ double pll_core_root_loglikelihood_repeats_avx2(unsigned int states,
                                                 const unsigned int * scaler,
                                                 double * const * frequencies,
                                                 const double * rate_weights,
-                                                const unsigned int * pattern_weights,
+                                                const double * pattern_weights,
                                                 const double * invar_proportion,
                                                 const int * invar_indices,
                                                 const unsigned int * freqs_indices,
@@ -2351,7 +2351,7 @@ double pll_core_edge_loglikelihood_repeats_generic_avx2(unsigned int states,
                                                         const double * pmatrix,
                                                         double ** frequencies,
                                                         const double * rate_weights,
-                                                        const unsigned int * pattern_weights,
+                                                        const double * pattern_weights,
                                                         const double * invar_proportion,
                                                         const int * invar_indices,
                                                         const unsigned int * freqs_indices,