Functions
Optimized functions

Functions

static void newviewGTRGAMMA_GAPPED_SAVE (int tipCase, double *x1_start, double *x2_start, double *x3_start, double *EV, double *tipVector, int *ex3, unsigned char *tipX1, unsigned char *tipX2, const int n, double *left, double *right, int *wgt, int *scalerIncrement, const boolean fastScaling, unsigned int *x1_gap, unsigned int *x2_gap, unsigned int *x3_gap, double *x1_gapColumn, double *x2_gapColumn, double *x3_gapColumn)
 Computation of conditional likelihood arrray for GTR GAMMA with memory saving (Optimized SSE3 version for DNA data) More...
 
static void newviewGTRGAMMA (int tipCase, double *x1_start, double *x2_start, double *x3_start, double *EV, double *tipVector, int *ex3, unsigned char *tipX1, unsigned char *tipX2, const int n, double *left, double *right, int *wgt, int *scalerIncrement, const boolean fastScaling)
 Computation of conditional likelihood arrray for GTR GAMMA (Optimized SSE3 version for DNA data) More...
 
static void newviewGTRCAT (int tipCase, double *EV, int *cptr, double *x1_start, double *x2_start, double *x3_start, double *tipVector, int *ex3, unsigned char *tipX1, unsigned char *tipX2, int n, double *left, double *right, int *wgt, int *scalerIncrement, const boolean fastScaling)
 Computation of conditional likelihood arrray for GTR CAT (Optimized SSE3 version for DNA data) More...
 
static void newviewGTRCAT_SAVE (int tipCase, double *EV, int *cptr, double *x1_start, double *x2_start, double *x3_start, double *tipVector, int *ex3, unsigned char *tipX1, unsigned char *tipX2, int n, double *left, double *right, int *wgt, int *scalerIncrement, const boolean fastScaling, unsigned int *x1_gap, unsigned int *x2_gap, unsigned int *x3_gap, double *x1_gapColumn, double *x2_gapColumn, double *x3_gapColumn, const int maxCats)
 Computation of conditional likelihood arrray for GTR CAT with memory saving (Optimized SSE3 version for DNA data) More...
 
static void newviewGTRGAMMAPROT_GAPPED_SAVE (int tipCase, double *x1, double *x2, double *x3, double *extEV, double *tipVector, int *ex3, unsigned char *tipX1, unsigned char *tipX2, int n, double *left, double *right, int *wgt, int *scalerIncrement, const boolean fastScaling, unsigned int *x1_gap, unsigned int *x2_gap, unsigned int *x3_gap, double *x1_gapColumn, double *x2_gapColumn, double *x3_gapColumn)
 Computation of conditional likelihood arrray for GTR GAMMA with memory saving (Optimized SSE3 version for AA data) More...
 
static void newviewGTRGAMMAPROT (int tipCase, double *x1, double *x2, double *x3, double *extEV, double *tipVector, int *ex3, unsigned char *tipX1, unsigned char *tipX2, int n, double *left, double *right, int *wgt, int *scalerIncrement, const boolean fastScaling)
 Computation of conditional likelihood arrray for GTR GAMMA (Optimized SSE3 version for AA data) More...
 
static void newviewGTRCATPROT (int tipCase, double *extEV, int *cptr, double *x1, double *x2, double *x3, double *tipVector, int *ex3, unsigned char *tipX1, unsigned char *tipX2, int n, double *left, double *right, int *wgt, int *scalerIncrement, const boolean fastScaling)
 Computation of conditional likelihood arrray for GTR CAT (Optimized SSE3 version for AA data) More...
 
static void newviewGTRCATPROT_SAVE (int tipCase, double *extEV, int *cptr, double *x1, double *x2, double *x3, double *tipVector, int *ex3, unsigned char *tipX1, unsigned char *tipX2, int n, double *left, double *right, int *wgt, int *scalerIncrement, const boolean fastScaling, unsigned int *x1_gap, unsigned int *x2_gap, unsigned int *x3_gap, double *x1_gapColumn, double *x2_gapColumn, double *x3_gapColumn, const int maxCats)
 Computation of conditional likelihood arrray for GTR CAT with memory saving (Optimized SSE3 version for AA data) More...
 
static void newviewGTRGAMMAPROT_LG4 (int tipCase, double *x1, double *x2, double *x3, double *extEV[4], double *tipVector[4], int *ex3, unsigned char *tipX1, unsigned char *tipX2, int n, double *left, double *right, int *wgt, int *scalerIncrement, const boolean useFastScaling)
 Computation of conditional likelihood arrray for the GTR GAMMA and for the LG4 model (Optimized SSE3 version for AA data) More...
 

Detailed Description

This is the optimized functions group

Function Documentation

static void newviewGTRCAT ( int  tipCase,
double *  EV,
int *  cptr,
double *  x1_start,
double *  x2_start,
double *  x3_start,
double *  tipVector,
int *  ex3,
unsigned char *  tipX1,
unsigned char *  tipX2,
int  n,
double *  left,
double *  right,
int *  wgt,
int *  scalerIncrement,
const boolean  fastScaling 
)
static

Computation of conditional likelihood arrray for GTR CAT (Optimized SSE3 version for DNA data)

This is the SSE3 optimized version of newviewCAT_FLEX for computing the conditional likelihood arrays at some node p, given child nodes q and r using the CAT model of rate heterogeneity.

Note
For more details and function argument description check the function newviewCAT_FLEX

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static void newviewGTRCAT_SAVE ( int  tipCase,
double *  EV,
int *  cptr,
double *  x1_start,
double *  x2_start,
double *  x3_start,
double *  tipVector,
int *  ex3,
unsigned char *  tipX1,
unsigned char *  tipX2,
int  n,
double *  left,
double *  right,
int *  wgt,
int *  scalerIncrement,
const boolean  fastScaling,
unsigned int *  x1_gap,
unsigned int *  x2_gap,
unsigned int *  x3_gap,
double *  x1_gapColumn,
double *  x2_gapColumn,
double *  x3_gapColumn,
const int  maxCats 
)
static

Computation of conditional likelihood arrray for GTR CAT with memory saving (Optimized SSE3 version for DNA data)

This is the SSE3 optimized version of newviewCAT_FLEX for computing the conditional likelihood arrays at some node p, given child nodes q and r using the CAT model of rate heterogeneity. The memory saving technique is incorporated.

Note
For more details and function argument description check the function newviewCAT_FLEX

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static void newviewGTRCATPROT ( int  tipCase,
double *  extEV,
int *  cptr,
double *  x1,
double *  x2,
double *  x3,
double *  tipVector,
int *  ex3,
unsigned char *  tipX1,
unsigned char *  tipX2,
int  n,
double *  left,
double *  right,
int *  wgt,
int *  scalerIncrement,
const boolean  fastScaling 
)
static

Computation of conditional likelihood arrray for GTR CAT (Optimized SSE3 version for AA data)

This is the SSE3 optimized version of newviewCAT_FLEX for computing the conditional likelihood arrays at some node p, given child nodes q and r using the CAT model of rate heterogeneity.

Note
For more details and function argument description check the function newviewCAT_FLEX

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static void newviewGTRCATPROT_SAVE ( int  tipCase,
double *  extEV,
int *  cptr,
double *  x1,
double *  x2,
double *  x3,
double *  tipVector,
int *  ex3,
unsigned char *  tipX1,
unsigned char *  tipX2,
int  n,
double *  left,
double *  right,
int *  wgt,
int *  scalerIncrement,
const boolean  fastScaling,
unsigned int *  x1_gap,
unsigned int *  x2_gap,
unsigned int *  x3_gap,
double *  x1_gapColumn,
double *  x2_gapColumn,
double *  x3_gapColumn,
const int  maxCats 
)
static

Computation of conditional likelihood arrray for GTR CAT with memory saving (Optimized SSE3 version for AA data)

This is the SSE3 optimized version of newviewCAT_FLEX for computing the conditional likelihood arrays at some node p, given child nodes q and r using the CAT model of rate heterogeneity.

Note
For more details and function argument description check the function newviewCAT_FLEX

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static void newviewGTRGAMMA ( int  tipCase,
double *  x1_start,
double *  x2_start,
double *  x3_start,
double *  EV,
double *  tipVector,
int *  ex3,
unsigned char *  tipX1,
unsigned char *  tipX2,
const int  n,
double *  left,
double *  right,
int *  wgt,
int *  scalerIncrement,
const boolean  fastScaling 
)
static

Computation of conditional likelihood arrray for GTR GAMMA (Optimized SSE3 version for DNA data)

This is the SSE3 optimized version of newviewGAMMA_FLEX for computing the conditional likelihood arrays at some node p, given child nodes q and r using the GAMMA model of rate heterogeneity.

Note
For more details and function argument description check the function newviewGAMMA_FLEX

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static void newviewGTRGAMMA_GAPPED_SAVE ( int  tipCase,
double *  x1_start,
double *  x2_start,
double *  x3_start,
double *  EV,
double *  tipVector,
int *  ex3,
unsigned char *  tipX1,
unsigned char *  tipX2,
const int  n,
double *  left,
double *  right,
int *  wgt,
int *  scalerIncrement,
const boolean  fastScaling,
unsigned int *  x1_gap,
unsigned int *  x2_gap,
unsigned int *  x3_gap,
double *  x1_gapColumn,
double *  x2_gapColumn,
double *  x3_gapColumn 
)
static

Computation of conditional likelihood arrray for GTR GAMMA with memory saving (Optimized SSE3 version for DNA data)

This is the SSE3 optimized version of newviewGAMMA_FLEX for computing the conditional likelihood arrays at some node p, given child nodes q and r using the GAMMA model of rate heterogeneity. The memory saving technique is incorporated.

Note
For more details and function argument description check the function newviewGAMMA_FLEX

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static void newviewGTRGAMMAPROT ( int  tipCase,
double *  x1,
double *  x2,
double *  x3,
double *  extEV,
double *  tipVector,
int *  ex3,
unsigned char *  tipX1,
unsigned char *  tipX2,
int  n,
double *  left,
double *  right,
int *  wgt,
int *  scalerIncrement,
const boolean  fastScaling 
)
static

Computation of conditional likelihood arrray for GTR GAMMA (Optimized SSE3 version for AA data)

This is the SSE3 optimized version of newviewGAMMA_FLEX for computing the conditional likelihood arrays at some node p, given child nodes q and r using the GAMMA model of rate heterogeneity.

Note
For more details and function argument description check the function newviewGAMMA_FLEX

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static void newviewGTRGAMMAPROT_GAPPED_SAVE ( int  tipCase,
double *  x1,
double *  x2,
double *  x3,
double *  extEV,
double *  tipVector,
int *  ex3,
unsigned char *  tipX1,
unsigned char *  tipX2,
int  n,
double *  left,
double *  right,
int *  wgt,
int *  scalerIncrement,
const boolean  fastScaling,
unsigned int *  x1_gap,
unsigned int *  x2_gap,
unsigned int *  x3_gap,
double *  x1_gapColumn,
double *  x2_gapColumn,
double *  x3_gapColumn 
)
static

Computation of conditional likelihood arrray for GTR GAMMA with memory saving (Optimized SSE3 version for AA data)

This is the SSE3 optimized version of newviewGAMMA_FLEX for computing the conditional likelihood arrays at some node p, given child nodes q and r using the GAMMA model of rate heterogeneity. The memory saving technique is incorporated.

Note
For more details and function argument description check the function newviewGAMMA_FLEX

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static void newviewGTRGAMMAPROT_LG4 ( int  tipCase,
double *  x1,
double *  x2,
double *  x3,
double *  extEV[4],
double *  tipVector[4],
int *  ex3,
unsigned char *  tipX1,
unsigned char *  tipX2,
int  n,
double *  left,
double *  right,
int *  wgt,
int *  scalerIncrement,
const boolean  useFastScaling 
)
static

Computation of conditional likelihood arrray for the GTR GAMMA and for the LG4 model (Optimized SSE3 version for AA data)

This is the SSE3 optimized version of newviewGAMMA_FLEX for computing the conditional likelihood arrays at some node p, given child nodes q and r using the GAMMA model of rate heterogeneity and the LG4 model of evolution. Note that the original unoptimized function does not incorporate the LG4 model.

Note
For more details and function argument description check the function newviewGAMMA_FLEX

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