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40 lines
1.1 KiB
C
40 lines
1.1 KiB
C
// $Id: distanceBasedSeqs2TreeFactory.h 1941 2007-04-15 14:17:22Z privmane $
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#include "distanceBasedSeqs2Tree.h"
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#include "pairwiseGammaDistance.h"
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#include "nj.h"
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//using namespace std;
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#ifndef __DISTANCEBASEDSEQS2TREEFACTORY_H
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#define __DISTANCEBASEDSEQS2TREEFACTORY_H
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typedef enum {homogeneousRatesDTME,
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pairwiseGammaDTME,
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commonAlphaDTME,
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rate4siteDTME,
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posteriorDTME
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} distanceBasedMethod_t;
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distanceBasedSeqs2Tree* distanceBasedSeqs2TreeFactory(const distanceBasedMethod_t distanceBasedMethod,
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stochasticProcess& sp, // may change sp (alpha)
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const bool useJcDistance,
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const bool optimizeAlpha,
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const bool useSSRV,
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const double epsilonLikelihoodImprovement4iterNJ = 0.01,
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const double epsilonLikelihoodImprovement4pairwiseDistance = 0.0001,
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const double epsilonLikelihoodImprovement4alphaOptimiz = 0.01,
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const double epsilonLikelihoodImprovement4BBL = 0.01,
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const int maxIterationsBBL = 10);
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#endif
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