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Searched refs:gamma_median (Results 1 – 12 of 12) sorted by relevance

/dports/biology/iqtree/IQ-TREE-2.0.6/model/
H A Dmodelpomomixture.cpp36 …eGamma(num_rate_cats, Params::getInstance().gamma_shape, Params::getInstance().gamma_median, tree); in ModelPoMoMixture()
H A Dmodelfactory.cpp797 site_rate = new RateGammaInvar(num_rate_cats, gamma_shape, params.gamma_median, in ModelFactory()
804 site_rate = new RateGamma(num_rate_cats, gamma_shape, params.gamma_median, tree); in ModelFactory()
/dports/biology/iqtree/IQ-TREE-2.0.6/utils/
H A Dtools.h1523 bool gamma_median;
H A Dtools.cpp935 params.gamma_median = false; in parseArg()
2623 params.gamma_median = false; in parseArg()
2627 params.gamma_median = true; in parseArg()
/dports/biology/phyml/phyml-3.3.20200621/src/
H A Dcl.c518 io->mod->ras->gamma_median = 1; in Read_Command_Line()
H A Dmodels.c689 mod->ras->gamma_median); in Update_RAS()
H A Dm4.c348 …creteGamma(m4mod->h_fq,m4mod->multipl,m4mod->alpha,m4mod->alpha,m4mod->n_h,mod->ras->gamma_median); in M4_Update_Qmat()
H A Dutilities.h1046 …int gamma_median; /*! 1: use the median of each bin in the discrete gamma distribu… member
H A Dio.c2138 PhyML_Printf("\n. gamma_median=%d",mod->ras->gamma_median); in Print_Model()
2912 …tf("\n . 'Middle' of each rate class:\t\t\t %s",(io->mod->ras->gamma_median)?("median"):("m… in Print_Settings()
H A Dlk.c1921 mod->ras->alpha->v,mod->ras->n_catg,mod->ras->gamma_median); in Lk_Given_Two_Seq()
H A Dinit.c656 mod->ras->gamma_median = NO; in Set_Defaults_Model()
H A Dutilities.c3764 cpy->ras->gamma_median = ori->ras->gamma_median; in Record_Model()