93 …                     unsigned char *tipX1, int n, double *diagptable, const pllBoolean fastScaling,
98 static double evaluateGTRGAMMAPROT_GAPPED_SAVE (const pllBoolean fastScaling, int *ex1, int *ex2, i…
107 static double evaluateGTRGAMMAPROT (const pllBoolean fastScaling, int *ex1, int *ex2, int *wptr,
114 static double evaluateGTRCATPROT (const pllBoolean fastScaling, int *ex1, int *ex2, int *cptr, int …
121 static double evaluateGTRCATPROT_SAVE (const pllBoolean fastScaling, int *ex1, int *ex2, int *cptr,…
128 static double evaluateGTRCAT_SAVE (const pllBoolean fastScaling, int *ex1, int *ex2, int *cptr, int…
133 static double evaluateGTRGAMMA_GAPPED_SAVE(const pllBoolean fastScaling, int *ex1, int *ex2, int *w…
139 static double evaluateGTRGAMMA(const pllBoolean fastScaling, int *ex1, int *ex2, int *wptr,
145 static double evaluateGTRCAT (const pllBoolean fastScaling, int *ex1, int *ex2, int *cptr, int *wpt…
156 …              unsigned char *tipX1, const int n, double *diagptable, const pllBoolean fastScaling);
160 …              unsigned char *tipX1, int n, double *diagptable_start, const pllBoolean fastScaling);
581 static double evaluateGAMMA_FLEX(const pllBoolean fastScaling, int *ex1, int *ex2, int *wptr,  in evaluateGAMMA_FLEX()  argument
631       if(!fastScaling)  in evaluateGAMMA_FLEX()
659       if(!fastScaling)  in evaluateGAMMA_FLEX()
751 static double evaluateGAMMA_FLEX_SAVE(const pllBoolean fastScaling, int *ex1, int *ex2, int *wptr,  in evaluateGAMMA_FLEX_SAVE()  argument
811       if(!fastScaling)  in evaluateGAMMA_FLEX_SAVE()
852       if(!fastScaling)  in evaluateGAMMA_FLEX_SAVE()
933 static double evaluateCAT_FLEX (const pllBoolean fastScaling, int *ex1, int *ex2, int *cptr, int *w…  in evaluateCAT_FLEX()  argument
975        if(!fastScaling)  in evaluateCAT_FLEX()
1011       if(!fastScaling)  in evaluateCAT_FLEX()
1047 static double evaluateCAT_FLEX_SAVE (const pllBoolean fastScaling, int *ex1, int *ex2, int *cptr, i…  in evaluateCAT_FLEX_SAVE()  argument
1098        if(!fastScaling)  in evaluateCAT_FLEX_SAVE()
1148       if(!fastScaling)  in evaluateCAT_FLEX_SAVE()
1212     fastScaling = tr->fastScaling;  in pllEvaluateIterative()  local
1374                   if(!fastScaling)                    in pllEvaluateIterative()
1405                   if(!fastScaling)                    in pllEvaluateIterative()
1432               if(!fastScaling)  in pllEvaluateIterative()
1479 …partitionLikelihood = evaluateCAT_FLEX(fastScaling, ex1, ex2, pr->partitionData[model]->rateCatego…  in pllEvaluateIterative()
1483 …     partitionLikelihood = evaluateGAMMA_FLEX(fastScaling, ex1, ex2, pr->partitionData[model]->wgt,  in pllEvaluateIterative()
1500 …partitionLikelihood = evaluateCAT_FLEX_SAVE(fastScaling, ex1, ex2, pr->partitionData[model]->rateC…  in pllEvaluateIterative()
1505 …partitionLikelihood = evaluateCAT_FLEX(fastScaling, ex1, ex2, pr->partitionData[model]->rateCatego…  in pllEvaluateIterative()
1512 …partitionLikelihood = evaluateGAMMA_FLEX_SAVE(fastScaling, ex1, ex2, pr->partitionData[model]->wgt,  in pllEvaluateIterative()
1517 …     partitionLikelihood = evaluateGAMMA_FLEX(fastScaling, ex1, ex2, pr->partitionData[model]->wgt,  in pllEvaluateIterative()
1537 …                                                              tip, width, diagptable, fastScaling);  in pllEvaluateIterative()
1543 …                                             tip, width, diagptable, fastScaling);                   in pllEvaluateIterative()
1558                                               tip, width, diagptable, fastScaling);  in pllEvaluateIterative()
1563 …partitionLikelihood =  evaluateGTRCAT_SAVE(fastScaling, ex1, ex2, pr->partitionData[model]->rateCa…  in pllEvaluateIterative()
1567 …partitionLikelihood =  evaluateGTRCAT(fastScaling, ex1, ex2, pr->partitionData[model]->rateCategor…  in pllEvaluateIterative()
1574 …partitionLikelihood =  evaluateGTRGAMMA_GAPPED_SAVE(fastScaling, ex1, ex2, pr->partitionData[model…  in pllEvaluateIterative()
1579 …      partitionLikelihood =  evaluateGTRGAMMA(fastScaling, ex1, ex2, pr->partitionData[model]->wgt,  in pllEvaluateIterative()
1603                                               tip, width, diagptable, fastScaling);  in pllEvaluateIterative()
1619 …partitionLikelihood = evaluateGTRCATPROT_SAVE(fastScaling, ex1, ex2, pr->partitionData[model]->rat…  in pllEvaluateIterative()
1623 …partitionLikelihood = evaluateGTRCATPROT(fastScaling, ex1, ex2, pr->partitionData[model]->rateCate…  in pllEvaluateIterative()
1630 …partitionLikelihood = evaluateGTRGAMMAPROT_GAPPED_SAVE(fastScaling, ex1, ex2, pr->partitionData[mo…  in pllEvaluateIterative()
1641 …   partitionLikelihood = evaluateGTRGAMMAPROT(fastScaling, ex1, ex2, pr->partitionData[model]->wgt,  in pllEvaluateIterative()
1670           if(fastScaling)  in pllEvaluateIterative()
1830     assert(!(tr->fastScaling));   in pllEvaluateLikelihood()
2102 …               unsigned char *tipX1, int n, double *diagptable_start, const pllBoolean fastScaling)  in evaluateGTRCAT_BINARY()  argument
2126           if(fastScaling)  in evaluateGTRCAT_BINARY()
2134           if(fastScaling)  in evaluateGTRCAT_BINARY()
2157           if(fastScaling)  in evaluateGTRCAT_BINARY()
2165           if(fastScaling)  in evaluateGTRCAT_BINARY()
2182 …               unsigned char *tipX1, const int n, double *diagptable, const pllBoolean fastScaling)  in evaluateGTRGAMMA_BINARY()  argument
2218           if(fastScaling)  in evaluateGTRGAMMA_BINARY()
2227           if(fastScaling)  in evaluateGTRGAMMA_BINARY()
2265           if(fastScaling)  in evaluateGTRGAMMA_BINARY()
2274           if(fastScaling)  in evaluateGTRGAMMA_BINARY()
2306 …                     unsigned char *tipX1, int n, double *diagptable, const pllBoolean fastScaling,  in evaluateGTRGAMMAPROT_LG4()  argument
2357           if(fastScaling)  in evaluateGTRGAMMAPROT_LG4()
2408           if(fastScaling)  in evaluateGTRGAMMAPROT_LG4()
2430 static double evaluateGTRGAMMAPROT_GAPPED_SAVE (const pllBoolean fastScaling, int *ex1, int *ex2, i…  in evaluateGTRGAMMAPROT_GAPPED_SAVE()  argument
2479       if(!fastScaling)  in evaluateGTRGAMMAPROT_GAPPED_SAVE()
2526        if(!fastScaling)  in evaluateGTRGAMMAPROT_GAPPED_SAVE()
2550 static double evaluateGTRGAMMAPROT (const pllBoolean fastScaling, int *ex1, int *ex2, int *wptr,  in evaluateGTRGAMMAPROT()  argument
2581       if(!fastScaling)  in evaluateGTRGAMMAPROT()
2612        if(!fastScaling)  in evaluateGTRGAMMAPROT()
2635 static double evaluateGTRCATPROT (const pllBoolean fastScaling, int *ex1, int *ex2, int *cptr, int …  in evaluateGTRCATPROT()  argument
2670       if(!fastScaling)  in evaluateGTRCATPROT()
2703       if(!fastScaling)  in evaluateGTRCATPROT()
2725 static double evaluateGTRCATPROT_SAVE (const pllBoolean fastScaling, int *ex1, int *ex2, int *cptr,…  in evaluateGTRCATPROT_SAVE()  argument
2774       if(!fastScaling)  in evaluateGTRCATPROT_SAVE()
2820       if(!fastScaling)  in evaluateGTRCATPROT_SAVE()
2842 static double evaluateGTRCAT_SAVE (const pllBoolean fastScaling, int *ex1, int *ex2, int *cptr, int…  in evaluateGTRCAT_SAVE()  argument
2892       if(!fastScaling)  in evaluateGTRCAT_SAVE()
2945        if(!fastScaling)  in evaluateGTRCAT_SAVE()
2967 static double evaluateGTRGAMMA_GAPPED_SAVE(const pllBoolean fastScaling, int *ex1, int *ex2, int *w…  in evaluateGTRGAMMA_GAPPED_SAVE()  argument
3027        if(!fastScaling)  in evaluateGTRGAMMA_GAPPED_SAVE()
3085       if(!fastScaling)  in evaluateGTRGAMMA_GAPPED_SAVE()
3107 static double evaluateGTRGAMMA(const pllBoolean fastScaling, int *ex1, int *ex2, int *wptr,  in evaluateGTRGAMMA()  argument
3156        if(!fastScaling)  in evaluateGTRGAMMA()
3203       if(!fastScaling)  in evaluateGTRGAMMA()
3226 static double evaluateGTRCAT (const pllBoolean fastScaling, int *ex1, int *ex2, int *cptr, int *wpt…  in evaluateGTRCAT()  argument
3265        if(!fastScaling)  in evaluateGTRCAT()
3304       if(!fastScaling)  in evaluateGTRCAT()