diff --git a/README b/README index 37694ebb6e2c466cf349cdb167595904e6ca027f..b56f95e2eb114980d47d121fc0cf21e92bbc851b 100644 --- a/README +++ b/README @@ -126,6 +126,9 @@ By adding progname into the list all_estimators the tool is added to phybema. - src_external: contains the source code of the software TreeCmp. The orginal source code can be found at https://eti.pg.edu.pl/treecmp/. + + - doc: The EvolSimulator (http://bioinformatics.org.au/tools/evolsim/) configuration files + used for simulating the datasets - testdata: provides real and simulated data diff --git a/doc/EvolSimconfigs/evolSimconfig_Gendivm01.txt b/doc/EvolSimconfigs/evolSimconfig_Gendivm01.txt new file mode 100755 index 0000000000000000000000000000000000000000..18640205c92a50c1a94fe8dd6e389a70f6b119f6 --- /dev/null +++ b/doc/EvolSimconfigs/evolSimconfig_Gendivm01.txt @@ -0,0 +1,156 @@ +numIterations(x>0) + 5000 +outInterval(x>0,_may_be_>numIterations) + 5001 +rateAndBiasAdjustFrequency(x>0) + 10 +preferredMinNumLineages(x>0) + 25 +maxNumLineages(x>=preferredMinNumLineages) + 35 +speciationAndExtinctionProb(0.0<=x<1.0) + 0.5 +speciationModel{0,1,2} + 1 +selectionModel{0,1,2,3,4} + 0 +numberOfHabitats(x>=1) + 10 +numberOfHabitatNiches(x>=numberOfHabitats) + 100 +numberOfHabitatSpaces(x>=maxNumLineages_&&_x>=numberOfHabitatNiches) + 1000 +probMigrationPerIter(0.0<=x<=1.0) + 0.5 +paralogUsefulnessFactor(x>0.0) + 2.0 +meanNumLGTperIteration(x>=0.0) + 0.0 +exactPropGlobalReq(0.0<=x<=1.0) + 0.02 +meanPropHabReq(0.0<=x<=1.0) + 0.02 +meanPropNicheReq(0.0<=x<=1.0) + 0.01 + +minGenomeSize(x>0) + 2000 +maxGenomeSize(x>=minGenomeSize) + 3000 +initialTargetSize(minGenomeSize<=x<=maxGenomeSize) + 2000 +sizeAdjFactor(x>=0.0) + 1.0 +targetSizeDriftFactor(x>=0.0) + 5.0 + +duplicabilityDriftFactor(0.0<=x<=1.0) + 0.005 +inertiaDriftFactor(0.0<=x<=1.0) + 0.005 +resistanceAdjFactor(0.0<=x<=1.0) + 0.05 +selectiveDriftFactor(0.0<=x<=1.0) + 0.0005 +selectiveDriftBias(0.0<=x<=1.0) + 0.8 +maxInitialSelectivePressure(0.0<x<=1.0) + 0.2 +goodMutationProb(0.0<=x<=1.0) + 0.05 +mutationRateDriftFactor(0.0<=x<=1.0) + 0.005 +minMutationRate(0.0<x<1.0) + 0.1 +maxMutationRate(minMutationRate<=x<1.0) + 0.1 +mutationRate(0.0<x<1.0) + 0.1 +transitionProbDriftFactor(0.0<=x<=1.0) + 0.0005 +minTransitionProb(0.0<x<1.0) + 0.5 +maxTransitionProb(minTransitionProb<=x<1.0) + 0.9 +transitionProb(0.0<x<1.0) + 0.666667 +gcBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minGCbias(0.0<x<1.0) + 0.25 +maxGCbias(minGCbias<=x<1.0) + 0.75 +gcBias(0.0<x<1.0) + 0.5 +purineBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minPurineBias(0.0<x<1.0) + 0.1 +maxPurineBias(minPurineBias<=x<1.0) + 0.25 +purineBias(0.0<x<1.0) + 0.1 + +randomLGTProb(0.0<=x<=1.0) + 0.0 +divergenceLGTProb(0.0<=x<=1.0) + 0.0 +geneCompLGTProb(0.0<=x<=1.0) + 0.0 +gcLGTProb(0.0<=x<=1.0) + 0.0 +habitatLGTProb(0.0<=x<=1.0) + 0.0 + +divergenceFactor(x>0.0,_normally_x<=numIterations) + 5000.0 +geneCompSimilarityFactor(0.0<=x<1.0) + 0.9 +gcSimilarityFactor(0.0<x<=1.0) + 0.9 +orthologReplacementProbability(0.0<=x<=1.0) + 1.0 +lgtReceptivityDriftFactor(0.0<=x<=1.0) + 0.005 +lgtMinReceptivity(0.0<=x<=1.0) + 0 +lgtMaxReceptivity(lgtMinReceptivity<=x<=1.0) + 0 +lgtReceptivity(0<=x<=1.0) + 0 + +minGeneSize(x>0) + 80 +maxGeneSize(x>=minGeneSize) + 500 +substitutionMatrix(list_of_400_positive_values_<=2.0,_ACDEFGHIKLMNPQRSTVWY_x_ACDEFGHIKLMNPQRSTVWY) +2.0 0.0396598 0.0843124 0.183797 0.0161794 0.235889 0.0154872 0.0187403 0.112429 0.0686077 0.0348512 0.0398593 0.131665 0.0667422 0.0485074 0.46866 0.258829 0.284435 0.00325504 0.0169835 +0.177941 2.0 0.00345635 0.00247935 0.0305933 0.0510623 0.0121654 0.0164915 0.00918444 0.066258 0.0152309 0.0207374 0.0100133 0.00725879 0.0464512 0.195715 0.0625971 0.142095 0.0206314 0.0383665 +0.128036 0.00116986 2.0 0.71693 0.00359188 0.144123 0.0454752 0.00382271 0.0595295 0.0146219 0.00404697 0.424466 0.0388056 0.0453065 0.0129545 0.149013 0.0457432 0.0215998 0.00373363 0.0229784 +0.274238 0.00082452 0.704411 2.0 0.00623626 0.0945269 0.0278529 0.0123487 0.320617 0.0265977 0.0122915 0.0740508 0.0624534 0.401766 0.0386212 0.0980118 0.100398 0.0834769 0.00450443 0.0138489 +0.0364693 0.0153698 0.00533148 0.00942109 2.0 0.00831369 0.0331958 0.102697 0.0110207 0.364693 0.046441 0.00751784 0.0147764 0.0073398 0.00903282 0.075904 0.0209765 0.092149 0.0440105 0.455339 +0.245455 0.0118424 0.0987547 0.065922 0.00383789 2.0 0.0121868 0.00295159 0.0463426 0.0105699 0.00679084 0.0879949 0.022293 0.0242444 0.0514178 0.186561 0.0275574 0.02655 0.00969561 0.0073091 +0.0549141 0.0096142 0.106181 0.06619 0.052219 0.0415277 2.0 0.013395 0.110465 0.0861162 0.0157637 0.309298 0.0637204 0.315429 0.18795 0.10291 0.0577555 0.0167821 0.00755458 0.273265 +0.0334964 0.00656987 0.00449938 0.0147928 0.0814349 0.00507005 0.00675232 2.0 0.0401737 0.546732 0.166064 0.0433295 0.0091461 0.00836791 0.0164437 0.0444136 0.177933 1.10899 0.00611352 0.0296423 +0.157016 0.00285886 0.0547468 0.300098 0.00682827 0.0621988 0.0435088 0.0313897 2.0 0.0444071 0.0364418 0.235475 0.0509706 0.286105 0.470625 0.134466 0.169247 0.0433079 0.00395627 0.00940156 +0.0689411 0.0148395 0.00967539 0.0179127 0.16258 0.0102073 0.024405 0.307368 0.0319516 2.0 0.189333 0.0102827 0.0380606 0.0638694 0.0437672 0.0479311 0.0398562 0.255272 0.0191421 0.0281219 +0.154803 0.0150787 0.0118373 0.0365915 0.0915163 0.0289883 0.0197474 0.412684 0.115904 0.83692 2.0 0.0154967 0.0156811 0.113509 0.06008 0.0686705 0.185005 0.29187 0.0148378 0.0302255 +0.0883341 0.010243 0.619444 0.109987 0.00739138 0.18741 0.193315 0.0537232 0.373662 0.0226778 0.00773169 2.0 0.017855 0.11339 0.0558749 0.55256 0.247719 0.027826 0.00206917 0.0766156 +0.249237 0.0042247 0.0483724 0.0792336 0.0124092 0.0405553 0.034018 0.0096863 0.069087 0.071699 0.00668276 0.0152512 2.0 0.068562 0.059757 0.224304 0.0970571 0.0446482 0.00401093 0.0152417 +0.15742 0.00381591 0.0703689 0.635103 0.00768029 0.0549548 0.209821 0.0110422 0.48319 0.149916 0.0602735 0.12068 0.085428 2.0 0.266954 0.14305 0.104689 0.042719 0.00620714 0.0160646 +0.0955629 0.0203964 0.0168059 0.0509939 0.00789476 0.0973488 0.104427 0.0181242 0.663882 0.0858074 0.026647 0.0496706 0.062191 0.222976 2.0 0.170206 0.0676525 0.03571 0.0334881 0.0269165 +0.584009 0.0543576 0.122277 0.081856 0.0419623 0.223418 0.0361666 0.030964 0.119979 0.0594392 0.019265 0.310701 0.147657 0.0755769 0.10766 2.0 0.53423 0.0330003 0.015069 0.0555211 +0.367495 0.0198092 0.0427685 0.0955377 0.0132131 0.037602 0.023127 0.141342 0.172065 0.0563155 0.0591369 0.158708 0.0727985 0.0630201 0.0487573 0.608702 2.0 0.196839 0.00318976 0.02054 +0.347553 0.0386982 0.0173799 0.0683621 0.0499532 0.0311773 0.00578328 0.758134 0.0378913 0.310411 0.0802907 0.0153423 0.0288204 0.022131 0.0221486 0.0323591 0.169399 2.0 0.0105123 0.0222037 +0.0196009 0.0276901 0.0148051 0.0181791 0.117574 0.0561089 0.0128298 0.0205964 0.0170585 0.114711 0.0201153 0.00562236 0.0127592 0.0158472 0.10236 0.0728189 0.0135282 0.0518061 2.0 0.17534 +0.0417087 0.0210004 0.0371604 0.0227943 0.4961 0.0172504 0.189266 0.0407279 0.0165324 0.0687289 0.0167114 0.0849022 0.0197739 0.0167267 0.0335535 0.10942 0.0355275 0.0446259 0.0715091 2.0 +numAuxiliaryMatrices(x>0) + 1000 +auxMatrixScaleFactor(x>=1.0) + 2.0 +numProteinTypes(x=0_then_fnaFileName,or,x>0_then_that_many_numOfProteinType_+_set_of_frequencies) + 1 +numOfProteinType[i]_(x>0,_sum_of_numOfProteinType[i=1_to_i=numProteinTypes]_>=minGenomeSize_and_<=maxGenomeSize) + 2500 +freqOf_ACDEFGHIKLMNPQRSTVWY(list_of_20_positive_values_whose_sum_is_1.0) +0.0866279 0.043972 0.0390894 0.0570451 0.0193078 0.0367281 0.0580589 0.0832518 0.0244313 0.048466 0.086209 0.0620286 0.0195027 0.0384319 0.0457631 0.0695179 0.0610127 0.0143859 0.0352742 0.0708956 diff --git a/doc/EvolSimconfigs/evolSimconfig_Gendivm02.txt b/doc/EvolSimconfigs/evolSimconfig_Gendivm02.txt new file mode 100755 index 0000000000000000000000000000000000000000..c56521e19ec17f121229b3cd56417892092c3813 --- /dev/null +++ b/doc/EvolSimconfigs/evolSimconfig_Gendivm02.txt @@ -0,0 +1,156 @@ +numIterations(x>0) + 5000 +outInterval(x>0,_may_be_>numIterations) + 5001 +rateAndBiasAdjustFrequency(x>0) + 10 +preferredMinNumLineages(x>0) + 25 +maxNumLineages(x>=preferredMinNumLineages) + 35 +speciationAndExtinctionProb(0.0<=x<1.0) + 0.5 +speciationModel{0,1,2} + 1 +selectionModel{0,1,2,3,4} + 0 +numberOfHabitats(x>=1) + 10 +numberOfHabitatNiches(x>=numberOfHabitats) + 100 +numberOfHabitatSpaces(x>=maxNumLineages_&&_x>=numberOfHabitatNiches) + 1000 +probMigrationPerIter(0.0<=x<=1.0) + 0.5 +paralogUsefulnessFactor(x>0.0) + 2.0 +meanNumLGTperIteration(x>=0.0) + 0.0 +exactPropGlobalReq(0.0<=x<=1.0) + 0.02 +meanPropHabReq(0.0<=x<=1.0) + 0.02 +meanPropNicheReq(0.0<=x<=1.0) + 0.01 + +minGenomeSize(x>0) + 2000 +maxGenomeSize(x>=minGenomeSize) + 3000 +initialTargetSize(minGenomeSize<=x<=maxGenomeSize) + 2000 +sizeAdjFactor(x>=0.0) + 1.0 +targetSizeDriftFactor(x>=0.0) + 5.0 + +duplicabilityDriftFactor(0.0<=x<=1.0) + 0.005 +inertiaDriftFactor(0.0<=x<=1.0) + 0.005 +resistanceAdjFactor(0.0<=x<=1.0) + 0.05 +selectiveDriftFactor(0.0<=x<=1.0) + 0.0005 +selectiveDriftBias(0.0<=x<=1.0) + 0.8 +maxInitialSelectivePressure(0.0<x<=1.0) + 0.2 +goodMutationProb(0.0<=x<=1.0) + 0.05 +mutationRateDriftFactor(0.0<=x<=1.0) + 0.005 +minMutationRate(0.0<x<1.0) + 0.2 +maxMutationRate(minMutationRate<=x<1.0) + 0.2 +mutationRate(0.0<x<1.0) + 0.2 +transitionProbDriftFactor(0.0<=x<=1.0) + 0.0005 +minTransitionProb(0.0<x<1.0) + 0.5 +maxTransitionProb(minTransitionProb<=x<1.0) + 0.9 +transitionProb(0.0<x<1.0) + 0.666667 +gcBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minGCbias(0.0<x<1.0) + 0.25 +maxGCbias(minGCbias<=x<1.0) + 0.75 +gcBias(0.0<x<1.0) + 0.5 +purineBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minPurineBias(0.0<x<1.0) + 0.1 +maxPurineBias(minPurineBias<=x<1.0) + 0.25 +purineBias(0.0<x<1.0) + 0.1 + +randomLGTProb(0.0<=x<=1.0) + 0.0 +divergenceLGTProb(0.0<=x<=1.0) + 0.0 +geneCompLGTProb(0.0<=x<=1.0) + 0.0 +gcLGTProb(0.0<=x<=1.0) + 0.0 +habitatLGTProb(0.0<=x<=1.0) + 0.0 + +divergenceFactor(x>0.0,_normally_x<=numIterations) + 5000.0 +geneCompSimilarityFactor(0.0<=x<1.0) + 0.9 +gcSimilarityFactor(0.0<x<=1.0) + 0.9 +orthologReplacementProbability(0.0<=x<=1.0) + 1.0 +lgtReceptivityDriftFactor(0.0<=x<=1.0) + 0.005 +lgtMinReceptivity(0.0<=x<=1.0) + 0 +lgtMaxReceptivity(lgtMinReceptivity<=x<=1.0) + 0 +lgtReceptivity(0<=x<=1.0) + 0 + +minGeneSize(x>0) + 80 +maxGeneSize(x>=minGeneSize) + 500 +substitutionMatrix(list_of_400_positive_values_<=2.0,_ACDEFGHIKLMNPQRSTVWY_x_ACDEFGHIKLMNPQRSTVWY) +2.0 0.0396598 0.0843124 0.183797 0.0161794 0.235889 0.0154872 0.0187403 0.112429 0.0686077 0.0348512 0.0398593 0.131665 0.0667422 0.0485074 0.46866 0.258829 0.284435 0.00325504 0.0169835 +0.177941 2.0 0.00345635 0.00247935 0.0305933 0.0510623 0.0121654 0.0164915 0.00918444 0.066258 0.0152309 0.0207374 0.0100133 0.00725879 0.0464512 0.195715 0.0625971 0.142095 0.0206314 0.0383665 +0.128036 0.00116986 2.0 0.71693 0.00359188 0.144123 0.0454752 0.00382271 0.0595295 0.0146219 0.00404697 0.424466 0.0388056 0.0453065 0.0129545 0.149013 0.0457432 0.0215998 0.00373363 0.0229784 +0.274238 0.00082452 0.704411 2.0 0.00623626 0.0945269 0.0278529 0.0123487 0.320617 0.0265977 0.0122915 0.0740508 0.0624534 0.401766 0.0386212 0.0980118 0.100398 0.0834769 0.00450443 0.0138489 +0.0364693 0.0153698 0.00533148 0.00942109 2.0 0.00831369 0.0331958 0.102697 0.0110207 0.364693 0.046441 0.00751784 0.0147764 0.0073398 0.00903282 0.075904 0.0209765 0.092149 0.0440105 0.455339 +0.245455 0.0118424 0.0987547 0.065922 0.00383789 2.0 0.0121868 0.00295159 0.0463426 0.0105699 0.00679084 0.0879949 0.022293 0.0242444 0.0514178 0.186561 0.0275574 0.02655 0.00969561 0.0073091 +0.0549141 0.0096142 0.106181 0.06619 0.052219 0.0415277 2.0 0.013395 0.110465 0.0861162 0.0157637 0.309298 0.0637204 0.315429 0.18795 0.10291 0.0577555 0.0167821 0.00755458 0.273265 +0.0334964 0.00656987 0.00449938 0.0147928 0.0814349 0.00507005 0.00675232 2.0 0.0401737 0.546732 0.166064 0.0433295 0.0091461 0.00836791 0.0164437 0.0444136 0.177933 1.10899 0.00611352 0.0296423 +0.157016 0.00285886 0.0547468 0.300098 0.00682827 0.0621988 0.0435088 0.0313897 2.0 0.0444071 0.0364418 0.235475 0.0509706 0.286105 0.470625 0.134466 0.169247 0.0433079 0.00395627 0.00940156 +0.0689411 0.0148395 0.00967539 0.0179127 0.16258 0.0102073 0.024405 0.307368 0.0319516 2.0 0.189333 0.0102827 0.0380606 0.0638694 0.0437672 0.0479311 0.0398562 0.255272 0.0191421 0.0281219 +0.154803 0.0150787 0.0118373 0.0365915 0.0915163 0.0289883 0.0197474 0.412684 0.115904 0.83692 2.0 0.0154967 0.0156811 0.113509 0.06008 0.0686705 0.185005 0.29187 0.0148378 0.0302255 +0.0883341 0.010243 0.619444 0.109987 0.00739138 0.18741 0.193315 0.0537232 0.373662 0.0226778 0.00773169 2.0 0.017855 0.11339 0.0558749 0.55256 0.247719 0.027826 0.00206917 0.0766156 +0.249237 0.0042247 0.0483724 0.0792336 0.0124092 0.0405553 0.034018 0.0096863 0.069087 0.071699 0.00668276 0.0152512 2.0 0.068562 0.059757 0.224304 0.0970571 0.0446482 0.00401093 0.0152417 +0.15742 0.00381591 0.0703689 0.635103 0.00768029 0.0549548 0.209821 0.0110422 0.48319 0.149916 0.0602735 0.12068 0.085428 2.0 0.266954 0.14305 0.104689 0.042719 0.00620714 0.0160646 +0.0955629 0.0203964 0.0168059 0.0509939 0.00789476 0.0973488 0.104427 0.0181242 0.663882 0.0858074 0.026647 0.0496706 0.062191 0.222976 2.0 0.170206 0.0676525 0.03571 0.0334881 0.0269165 +0.584009 0.0543576 0.122277 0.081856 0.0419623 0.223418 0.0361666 0.030964 0.119979 0.0594392 0.019265 0.310701 0.147657 0.0755769 0.10766 2.0 0.53423 0.0330003 0.015069 0.0555211 +0.367495 0.0198092 0.0427685 0.0955377 0.0132131 0.037602 0.023127 0.141342 0.172065 0.0563155 0.0591369 0.158708 0.0727985 0.0630201 0.0487573 0.608702 2.0 0.196839 0.00318976 0.02054 +0.347553 0.0386982 0.0173799 0.0683621 0.0499532 0.0311773 0.00578328 0.758134 0.0378913 0.310411 0.0802907 0.0153423 0.0288204 0.022131 0.0221486 0.0323591 0.169399 2.0 0.0105123 0.0222037 +0.0196009 0.0276901 0.0148051 0.0181791 0.117574 0.0561089 0.0128298 0.0205964 0.0170585 0.114711 0.0201153 0.00562236 0.0127592 0.0158472 0.10236 0.0728189 0.0135282 0.0518061 2.0 0.17534 +0.0417087 0.0210004 0.0371604 0.0227943 0.4961 0.0172504 0.189266 0.0407279 0.0165324 0.0687289 0.0167114 0.0849022 0.0197739 0.0167267 0.0335535 0.10942 0.0355275 0.0446259 0.0715091 2.0 +numAuxiliaryMatrices(x>0) + 1000 +auxMatrixScaleFactor(x>=1.0) + 2.0 +numProteinTypes(x=0_then_fnaFileName,or,x>0_then_that_many_numOfProteinType_+_set_of_frequencies) + 1 +numOfProteinType[i]_(x>0,_sum_of_numOfProteinType[i=1_to_i=numProteinTypes]_>=minGenomeSize_and_<=maxGenomeSize) + 2500 +freqOf_ACDEFGHIKLMNPQRSTVWY(list_of_20_positive_values_whose_sum_is_1.0) +0.0866279 0.043972 0.0390894 0.0570451 0.0193078 0.0367281 0.0580589 0.0832518 0.0244313 0.048466 0.086209 0.0620286 0.0195027 0.0384319 0.0457631 0.0695179 0.0610127 0.0143859 0.0352742 0.0708956 diff --git a/doc/EvolSimconfigs/evolSimconfig_Gendivm03.txt b/doc/EvolSimconfigs/evolSimconfig_Gendivm03.txt new file mode 100755 index 0000000000000000000000000000000000000000..fa2c470b8cf35b371af02542773de2cedbcd10d3 --- /dev/null +++ b/doc/EvolSimconfigs/evolSimconfig_Gendivm03.txt @@ -0,0 +1,156 @@ +numIterations(x>0) + 5000 +outInterval(x>0,_may_be_>numIterations) + 5001 +rateAndBiasAdjustFrequency(x>0) + 10 +preferredMinNumLineages(x>0) + 25 +maxNumLineages(x>=preferredMinNumLineages) + 35 +speciationAndExtinctionProb(0.0<=x<1.0) + 0.5 +speciationModel{0,1,2} + 1 +selectionModel{0,1,2,3,4} + 0 +numberOfHabitats(x>=1) + 10 +numberOfHabitatNiches(x>=numberOfHabitats) + 100 +numberOfHabitatSpaces(x>=maxNumLineages_&&_x>=numberOfHabitatNiches) + 1000 +probMigrationPerIter(0.0<=x<=1.0) + 0.5 +paralogUsefulnessFactor(x>0.0) + 2.0 +meanNumLGTperIteration(x>=0.0) + 0.0 +exactPropGlobalReq(0.0<=x<=1.0) + 0.02 +meanPropHabReq(0.0<=x<=1.0) + 0.02 +meanPropNicheReq(0.0<=x<=1.0) + 0.01 + +minGenomeSize(x>0) + 2000 +maxGenomeSize(x>=minGenomeSize) + 3000 +initialTargetSize(minGenomeSize<=x<=maxGenomeSize) + 2000 +sizeAdjFactor(x>=0.0) + 1.0 +targetSizeDriftFactor(x>=0.0) + 5.0 + +duplicabilityDriftFactor(0.0<=x<=1.0) + 0.005 +inertiaDriftFactor(0.0<=x<=1.0) + 0.005 +resistanceAdjFactor(0.0<=x<=1.0) + 0.05 +selectiveDriftFactor(0.0<=x<=1.0) + 0.0005 +selectiveDriftBias(0.0<=x<=1.0) + 0.8 +maxInitialSelectivePressure(0.0<x<=1.0) + 0.2 +goodMutationProb(0.0<=x<=1.0) + 0.05 +mutationRateDriftFactor(0.0<=x<=1.0) + 0.005 +minMutationRate(0.0<x<1.0) + 0.3 +maxMutationRate(minMutationRate<=x<1.0) + 0.3 +mutationRate(0.0<x<1.0) + 0.3 +transitionProbDriftFactor(0.0<=x<=1.0) + 0.0005 +minTransitionProb(0.0<x<1.0) + 0.5 +maxTransitionProb(minTransitionProb<=x<1.0) + 0.9 +transitionProb(0.0<x<1.0) + 0.666667 +gcBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minGCbias(0.0<x<1.0) + 0.25 +maxGCbias(minGCbias<=x<1.0) + 0.75 +gcBias(0.0<x<1.0) + 0.5 +purineBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minPurineBias(0.0<x<1.0) + 0.1 +maxPurineBias(minPurineBias<=x<1.0) + 0.25 +purineBias(0.0<x<1.0) + 0.1 + +randomLGTProb(0.0<=x<=1.0) + 0.0 +divergenceLGTProb(0.0<=x<=1.0) + 0.0 +geneCompLGTProb(0.0<=x<=1.0) + 0.0 +gcLGTProb(0.0<=x<=1.0) + 0.0 +habitatLGTProb(0.0<=x<=1.0) + 0.0 + +divergenceFactor(x>0.0,_normally_x<=numIterations) + 5000.0 +geneCompSimilarityFactor(0.0<=x<1.0) + 0.9 +gcSimilarityFactor(0.0<x<=1.0) + 0.9 +orthologReplacementProbability(0.0<=x<=1.0) + 1.0 +lgtReceptivityDriftFactor(0.0<=x<=1.0) + 0.005 +lgtMinReceptivity(0.0<=x<=1.0) + 0 +lgtMaxReceptivity(lgtMinReceptivity<=x<=1.0) + 0 +lgtReceptivity(0<=x<=1.0) + 0 + +minGeneSize(x>0) + 80 +maxGeneSize(x>=minGeneSize) + 500 +substitutionMatrix(list_of_400_positive_values_<=2.0,_ACDEFGHIKLMNPQRSTVWY_x_ACDEFGHIKLMNPQRSTVWY) +2.0 0.0396598 0.0843124 0.183797 0.0161794 0.235889 0.0154872 0.0187403 0.112429 0.0686077 0.0348512 0.0398593 0.131665 0.0667422 0.0485074 0.46866 0.258829 0.284435 0.00325504 0.0169835 +0.177941 2.0 0.00345635 0.00247935 0.0305933 0.0510623 0.0121654 0.0164915 0.00918444 0.066258 0.0152309 0.0207374 0.0100133 0.00725879 0.0464512 0.195715 0.0625971 0.142095 0.0206314 0.0383665 +0.128036 0.00116986 2.0 0.71693 0.00359188 0.144123 0.0454752 0.00382271 0.0595295 0.0146219 0.00404697 0.424466 0.0388056 0.0453065 0.0129545 0.149013 0.0457432 0.0215998 0.00373363 0.0229784 +0.274238 0.00082452 0.704411 2.0 0.00623626 0.0945269 0.0278529 0.0123487 0.320617 0.0265977 0.0122915 0.0740508 0.0624534 0.401766 0.0386212 0.0980118 0.100398 0.0834769 0.00450443 0.0138489 +0.0364693 0.0153698 0.00533148 0.00942109 2.0 0.00831369 0.0331958 0.102697 0.0110207 0.364693 0.046441 0.00751784 0.0147764 0.0073398 0.00903282 0.075904 0.0209765 0.092149 0.0440105 0.455339 +0.245455 0.0118424 0.0987547 0.065922 0.00383789 2.0 0.0121868 0.00295159 0.0463426 0.0105699 0.00679084 0.0879949 0.022293 0.0242444 0.0514178 0.186561 0.0275574 0.02655 0.00969561 0.0073091 +0.0549141 0.0096142 0.106181 0.06619 0.052219 0.0415277 2.0 0.013395 0.110465 0.0861162 0.0157637 0.309298 0.0637204 0.315429 0.18795 0.10291 0.0577555 0.0167821 0.00755458 0.273265 +0.0334964 0.00656987 0.00449938 0.0147928 0.0814349 0.00507005 0.00675232 2.0 0.0401737 0.546732 0.166064 0.0433295 0.0091461 0.00836791 0.0164437 0.0444136 0.177933 1.10899 0.00611352 0.0296423 +0.157016 0.00285886 0.0547468 0.300098 0.00682827 0.0621988 0.0435088 0.0313897 2.0 0.0444071 0.0364418 0.235475 0.0509706 0.286105 0.470625 0.134466 0.169247 0.0433079 0.00395627 0.00940156 +0.0689411 0.0148395 0.00967539 0.0179127 0.16258 0.0102073 0.024405 0.307368 0.0319516 2.0 0.189333 0.0102827 0.0380606 0.0638694 0.0437672 0.0479311 0.0398562 0.255272 0.0191421 0.0281219 +0.154803 0.0150787 0.0118373 0.0365915 0.0915163 0.0289883 0.0197474 0.412684 0.115904 0.83692 2.0 0.0154967 0.0156811 0.113509 0.06008 0.0686705 0.185005 0.29187 0.0148378 0.0302255 +0.0883341 0.010243 0.619444 0.109987 0.00739138 0.18741 0.193315 0.0537232 0.373662 0.0226778 0.00773169 2.0 0.017855 0.11339 0.0558749 0.55256 0.247719 0.027826 0.00206917 0.0766156 +0.249237 0.0042247 0.0483724 0.0792336 0.0124092 0.0405553 0.034018 0.0096863 0.069087 0.071699 0.00668276 0.0152512 2.0 0.068562 0.059757 0.224304 0.0970571 0.0446482 0.00401093 0.0152417 +0.15742 0.00381591 0.0703689 0.635103 0.00768029 0.0549548 0.209821 0.0110422 0.48319 0.149916 0.0602735 0.12068 0.085428 2.0 0.266954 0.14305 0.104689 0.042719 0.00620714 0.0160646 +0.0955629 0.0203964 0.0168059 0.0509939 0.00789476 0.0973488 0.104427 0.0181242 0.663882 0.0858074 0.026647 0.0496706 0.062191 0.222976 2.0 0.170206 0.0676525 0.03571 0.0334881 0.0269165 +0.584009 0.0543576 0.122277 0.081856 0.0419623 0.223418 0.0361666 0.030964 0.119979 0.0594392 0.019265 0.310701 0.147657 0.0755769 0.10766 2.0 0.53423 0.0330003 0.015069 0.0555211 +0.367495 0.0198092 0.0427685 0.0955377 0.0132131 0.037602 0.023127 0.141342 0.172065 0.0563155 0.0591369 0.158708 0.0727985 0.0630201 0.0487573 0.608702 2.0 0.196839 0.00318976 0.02054 +0.347553 0.0386982 0.0173799 0.0683621 0.0499532 0.0311773 0.00578328 0.758134 0.0378913 0.310411 0.0802907 0.0153423 0.0288204 0.022131 0.0221486 0.0323591 0.169399 2.0 0.0105123 0.0222037 +0.0196009 0.0276901 0.0148051 0.0181791 0.117574 0.0561089 0.0128298 0.0205964 0.0170585 0.114711 0.0201153 0.00562236 0.0127592 0.0158472 0.10236 0.0728189 0.0135282 0.0518061 2.0 0.17534 +0.0417087 0.0210004 0.0371604 0.0227943 0.4961 0.0172504 0.189266 0.0407279 0.0165324 0.0687289 0.0167114 0.0849022 0.0197739 0.0167267 0.0335535 0.10942 0.0355275 0.0446259 0.0715091 2.0 +numAuxiliaryMatrices(x>0) + 1000 +auxMatrixScaleFactor(x>=1.0) + 2.0 +numProteinTypes(x=0_then_fnaFileName,or,x>0_then_that_many_numOfProteinType_+_set_of_frequencies) + 1 +numOfProteinType[i]_(x>0,_sum_of_numOfProteinType[i=1_to_i=numProteinTypes]_>=minGenomeSize_and_<=maxGenomeSize) + 2500 +freqOf_ACDEFGHIKLMNPQRSTVWY(list_of_20_positive_values_whose_sum_is_1.0) +0.0866279 0.043972 0.0390894 0.0570451 0.0193078 0.0367281 0.0580589 0.0832518 0.0244313 0.048466 0.086209 0.0620286 0.0195027 0.0384319 0.0457631 0.0695179 0.0610127 0.0143859 0.0352742 0.0708956 diff --git a/doc/EvolSimconfigs/evolSimconfig_Gendivm04.txt b/doc/EvolSimconfigs/evolSimconfig_Gendivm04.txt new file mode 100755 index 0000000000000000000000000000000000000000..5ce599d632540cb37f81c3c13bf07574ca9645c5 --- /dev/null +++ b/doc/EvolSimconfigs/evolSimconfig_Gendivm04.txt @@ -0,0 +1,156 @@ +numIterations(x>0) + 5000 +outInterval(x>0,_may_be_>numIterations) + 5001 +rateAndBiasAdjustFrequency(x>0) + 10 +preferredMinNumLineages(x>0) + 25 +maxNumLineages(x>=preferredMinNumLineages) + 35 +speciationAndExtinctionProb(0.0<=x<1.0) + 0.5 +speciationModel{0,1,2} + 1 +selectionModel{0,1,2,3,4} + 0 +numberOfHabitats(x>=1) + 10 +numberOfHabitatNiches(x>=numberOfHabitats) + 100 +numberOfHabitatSpaces(x>=maxNumLineages_&&_x>=numberOfHabitatNiches) + 1000 +probMigrationPerIter(0.0<=x<=1.0) + 0.5 +paralogUsefulnessFactor(x>0.0) + 2.0 +meanNumLGTperIteration(x>=0.0) + 0.0 +exactPropGlobalReq(0.0<=x<=1.0) + 0.02 +meanPropHabReq(0.0<=x<=1.0) + 0.02 +meanPropNicheReq(0.0<=x<=1.0) + 0.01 + +minGenomeSize(x>0) + 2000 +maxGenomeSize(x>=minGenomeSize) + 3000 +initialTargetSize(minGenomeSize<=x<=maxGenomeSize) + 2000 +sizeAdjFactor(x>=0.0) + 1.0 +targetSizeDriftFactor(x>=0.0) + 5.0 + +duplicabilityDriftFactor(0.0<=x<=1.0) + 0.005 +inertiaDriftFactor(0.0<=x<=1.0) + 0.005 +resistanceAdjFactor(0.0<=x<=1.0) + 0.05 +selectiveDriftFactor(0.0<=x<=1.0) + 0.0005 +selectiveDriftBias(0.0<=x<=1.0) + 0.8 +maxInitialSelectivePressure(0.0<x<=1.0) + 0.2 +goodMutationProb(0.0<=x<=1.0) + 0.05 +mutationRateDriftFactor(0.0<=x<=1.0) + 0.005 +minMutationRate(0.0<x<1.0) + 0.4 +maxMutationRate(minMutationRate<=x<1.0) + 0.4 +mutationRate(0.0<x<1.0) + 0.4 +transitionProbDriftFactor(0.0<=x<=1.0) + 0.0005 +minTransitionProb(0.0<x<1.0) + 0.5 +maxTransitionProb(minTransitionProb<=x<1.0) + 0.9 +transitionProb(0.0<x<1.0) + 0.666667 +gcBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minGCbias(0.0<x<1.0) + 0.25 +maxGCbias(minGCbias<=x<1.0) + 0.75 +gcBias(0.0<x<1.0) + 0.5 +purineBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minPurineBias(0.0<x<1.0) + 0.1 +maxPurineBias(minPurineBias<=x<1.0) + 0.25 +purineBias(0.0<x<1.0) + 0.1 + +randomLGTProb(0.0<=x<=1.0) + 0.0 +divergenceLGTProb(0.0<=x<=1.0) + 0.0 +geneCompLGTProb(0.0<=x<=1.0) + 0.0 +gcLGTProb(0.0<=x<=1.0) + 0.0 +habitatLGTProb(0.0<=x<=1.0) + 0.0 + +divergenceFactor(x>0.0,_normally_x<=numIterations) + 5000.0 +geneCompSimilarityFactor(0.0<=x<1.0) + 0.9 +gcSimilarityFactor(0.0<x<=1.0) + 0.9 +orthologReplacementProbability(0.0<=x<=1.0) + 1.0 +lgtReceptivityDriftFactor(0.0<=x<=1.0) + 0.005 +lgtMinReceptivity(0.0<=x<=1.0) + 0 +lgtMaxReceptivity(lgtMinReceptivity<=x<=1.0) + 0 +lgtReceptivity(0<=x<=1.0) + 0 + +minGeneSize(x>0) + 80 +maxGeneSize(x>=minGeneSize) + 500 +substitutionMatrix(list_of_400_positive_values_<=2.0,_ACDEFGHIKLMNPQRSTVWY_x_ACDEFGHIKLMNPQRSTVWY) +2.0 0.0396598 0.0843124 0.183797 0.0161794 0.235889 0.0154872 0.0187403 0.112429 0.0686077 0.0348512 0.0398593 0.131665 0.0667422 0.0485074 0.46866 0.258829 0.284435 0.00325504 0.0169835 +0.177941 2.0 0.00345635 0.00247935 0.0305933 0.0510623 0.0121654 0.0164915 0.00918444 0.066258 0.0152309 0.0207374 0.0100133 0.00725879 0.0464512 0.195715 0.0625971 0.142095 0.0206314 0.0383665 +0.128036 0.00116986 2.0 0.71693 0.00359188 0.144123 0.0454752 0.00382271 0.0595295 0.0146219 0.00404697 0.424466 0.0388056 0.0453065 0.0129545 0.149013 0.0457432 0.0215998 0.00373363 0.0229784 +0.274238 0.00082452 0.704411 2.0 0.00623626 0.0945269 0.0278529 0.0123487 0.320617 0.0265977 0.0122915 0.0740508 0.0624534 0.401766 0.0386212 0.0980118 0.100398 0.0834769 0.00450443 0.0138489 +0.0364693 0.0153698 0.00533148 0.00942109 2.0 0.00831369 0.0331958 0.102697 0.0110207 0.364693 0.046441 0.00751784 0.0147764 0.0073398 0.00903282 0.075904 0.0209765 0.092149 0.0440105 0.455339 +0.245455 0.0118424 0.0987547 0.065922 0.00383789 2.0 0.0121868 0.00295159 0.0463426 0.0105699 0.00679084 0.0879949 0.022293 0.0242444 0.0514178 0.186561 0.0275574 0.02655 0.00969561 0.0073091 +0.0549141 0.0096142 0.106181 0.06619 0.052219 0.0415277 2.0 0.013395 0.110465 0.0861162 0.0157637 0.309298 0.0637204 0.315429 0.18795 0.10291 0.0577555 0.0167821 0.00755458 0.273265 +0.0334964 0.00656987 0.00449938 0.0147928 0.0814349 0.00507005 0.00675232 2.0 0.0401737 0.546732 0.166064 0.0433295 0.0091461 0.00836791 0.0164437 0.0444136 0.177933 1.10899 0.00611352 0.0296423 +0.157016 0.00285886 0.0547468 0.300098 0.00682827 0.0621988 0.0435088 0.0313897 2.0 0.0444071 0.0364418 0.235475 0.0509706 0.286105 0.470625 0.134466 0.169247 0.0433079 0.00395627 0.00940156 +0.0689411 0.0148395 0.00967539 0.0179127 0.16258 0.0102073 0.024405 0.307368 0.0319516 2.0 0.189333 0.0102827 0.0380606 0.0638694 0.0437672 0.0479311 0.0398562 0.255272 0.0191421 0.0281219 +0.154803 0.0150787 0.0118373 0.0365915 0.0915163 0.0289883 0.0197474 0.412684 0.115904 0.83692 2.0 0.0154967 0.0156811 0.113509 0.06008 0.0686705 0.185005 0.29187 0.0148378 0.0302255 +0.0883341 0.010243 0.619444 0.109987 0.00739138 0.18741 0.193315 0.0537232 0.373662 0.0226778 0.00773169 2.0 0.017855 0.11339 0.0558749 0.55256 0.247719 0.027826 0.00206917 0.0766156 +0.249237 0.0042247 0.0483724 0.0792336 0.0124092 0.0405553 0.034018 0.0096863 0.069087 0.071699 0.00668276 0.0152512 2.0 0.068562 0.059757 0.224304 0.0970571 0.0446482 0.00401093 0.0152417 +0.15742 0.00381591 0.0703689 0.635103 0.00768029 0.0549548 0.209821 0.0110422 0.48319 0.149916 0.0602735 0.12068 0.085428 2.0 0.266954 0.14305 0.104689 0.042719 0.00620714 0.0160646 +0.0955629 0.0203964 0.0168059 0.0509939 0.00789476 0.0973488 0.104427 0.0181242 0.663882 0.0858074 0.026647 0.0496706 0.062191 0.222976 2.0 0.170206 0.0676525 0.03571 0.0334881 0.0269165 +0.584009 0.0543576 0.122277 0.081856 0.0419623 0.223418 0.0361666 0.030964 0.119979 0.0594392 0.019265 0.310701 0.147657 0.0755769 0.10766 2.0 0.53423 0.0330003 0.015069 0.0555211 +0.367495 0.0198092 0.0427685 0.0955377 0.0132131 0.037602 0.023127 0.141342 0.172065 0.0563155 0.0591369 0.158708 0.0727985 0.0630201 0.0487573 0.608702 2.0 0.196839 0.00318976 0.02054 +0.347553 0.0386982 0.0173799 0.0683621 0.0499532 0.0311773 0.00578328 0.758134 0.0378913 0.310411 0.0802907 0.0153423 0.0288204 0.022131 0.0221486 0.0323591 0.169399 2.0 0.0105123 0.0222037 +0.0196009 0.0276901 0.0148051 0.0181791 0.117574 0.0561089 0.0128298 0.0205964 0.0170585 0.114711 0.0201153 0.00562236 0.0127592 0.0158472 0.10236 0.0728189 0.0135282 0.0518061 2.0 0.17534 +0.0417087 0.0210004 0.0371604 0.0227943 0.4961 0.0172504 0.189266 0.0407279 0.0165324 0.0687289 0.0167114 0.0849022 0.0197739 0.0167267 0.0335535 0.10942 0.0355275 0.0446259 0.0715091 2.0 +numAuxiliaryMatrices(x>0) + 1000 +auxMatrixScaleFactor(x>=1.0) + 2.0 +numProteinTypes(x=0_then_fnaFileName,or,x>0_then_that_many_numOfProteinType_+_set_of_frequencies) + 1 +numOfProteinType[i]_(x>0,_sum_of_numOfProteinType[i=1_to_i=numProteinTypes]_>=minGenomeSize_and_<=maxGenomeSize) + 2500 +freqOf_ACDEFGHIKLMNPQRSTVWY(list_of_20_positive_values_whose_sum_is_1.0) +0.0866279 0.043972 0.0390894 0.0570451 0.0193078 0.0367281 0.0580589 0.0832518 0.0244313 0.048466 0.086209 0.0620286 0.0195027 0.0384319 0.0457631 0.0695179 0.0610127 0.0143859 0.0352742 0.0708956 diff --git a/doc/EvolSimconfigs/evolSimconfig_LGTd1000.txt b/doc/EvolSimconfigs/evolSimconfig_LGTd1000.txt new file mode 100755 index 0000000000000000000000000000000000000000..e385e462ae3955a989c5db5a591d04205f3b3319 --- /dev/null +++ b/doc/EvolSimconfigs/evolSimconfig_LGTd1000.txt @@ -0,0 +1,156 @@ +numIterations(x>0) + 5000 +outInterval(x>0,_may_be_>numIterations) + 5001 +rateAndBiasAdjustFrequency(x>0) + 10 +preferredMinNumLineages(x>0) + 25 +maxNumLineages(x>=preferredMinNumLineages) + 35 +speciationAndExtinctionProb(0.0<=x<1.0) + 0.5 +speciationModel{0,1,2} + 1 +selectionModel{0,1,2,3,4} + 0 +numberOfHabitats(x>=1) + 10 +numberOfHabitatNiches(x>=numberOfHabitats) + 100 +numberOfHabitatSpaces(x>=maxNumLineages_&&_x>=numberOfHabitatNiches) + 1000 +probMigrationPerIter(0.0<=x<=1.0) + 0.5 +paralogUsefulnessFactor(x>0.0) + 2.0 +meanNumLGTperIteration(x>=0.0) + 5.0 +exactPropGlobalReq(0.0<=x<=1.0) + 0.02 +meanPropHabReq(0.0<=x<=1.0) + 0.02 +meanPropNicheReq(0.0<=x<=1.0) + 0.01 + +minGenomeSize(x>0) + 2000 +maxGenomeSize(x>=minGenomeSize) + 3000 +initialTargetSize(minGenomeSize<=x<=maxGenomeSize) + 2000 +sizeAdjFactor(x>=0.0) + 1.0 +targetSizeDriftFactor(x>=0.0) + 5.0 + +duplicabilityDriftFactor(0.0<=x<=1.0) + 0.005 +inertiaDriftFactor(0.0<=x<=1.0) + 0.005 +resistanceAdjFactor(0.0<=x<=1.0) + 0.05 +selectiveDriftFactor(0.0<=x<=1.0) + 0.0005 +selectiveDriftBias(0.0<=x<=1.0) + 0.8 +maxInitialSelectivePressure(0.0<x<=1.0) + 0.2 +goodMutationProb(0.0<=x<=1.0) + 0.05 +mutationRateDriftFactor(0.0<=x<=1.0) + 0.005 +minMutationRate(0.0<x<1.0) + 0.1 +maxMutationRate(minMutationRate<=x<1.0) + 0.1 +mutationRate(0.0<x<1.0) + 0.1 +transitionProbDriftFactor(0.0<=x<=1.0) + 0.0005 +minTransitionProb(0.0<x<1.0) + 0.5 +maxTransitionProb(minTransitionProb<=x<1.0) + 0.9 +transitionProb(0.0<x<1.0) + 0.666667 +gcBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minGCbias(0.0<x<1.0) + 0.25 +maxGCbias(minGCbias<=x<1.0) + 0.75 +gcBias(0.0<x<1.0) + 0.5 +purineBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minPurineBias(0.0<x<1.0) + 0.1 +maxPurineBias(minPurineBias<=x<1.0) + 0.25 +purineBias(0.0<x<1.0) + 0.1 + +randomLGTProb(0.0<=x<=1.0) + 0.0 +divergenceLGTProb(0.0<=x<=1.0) + 1.0 +geneCompLGTProb(0.0<=x<=1.0) + 0.0 +gcLGTProb(0.0<=x<=1.0) + 0.0 +habitatLGTProb(0.0<=x<=1.0) + 0.0 + +divergenceFactor(x>0.0,_normally_x<=numIterations) + 1000.0 +geneCompSimilarityFactor(0.0<=x<1.0) + 0.9 +gcSimilarityFactor(0.0<x<=1.0) + 0.9 +orthologReplacementProbability(0.0<=x<=1.0) + 1.0 +lgtReceptivityDriftFactor(0.0<=x<=1.0) + 0.005 +lgtMinReceptivity(0.0<=x<=1.0) + 1.0 +lgtMaxReceptivity(lgtMinReceptivity<=x<=1.0) + 1.0 +lgtReceptivity(0<=x<=1.0) + 1.0 + +minGeneSize(x>0) + 80 +maxGeneSize(x>=minGeneSize) + 500 +substitutionMatrix(list_of_400_positive_values_<=2.0,_ACDEFGHIKLMNPQRSTVWY_x_ACDEFGHIKLMNPQRSTVWY) +2.0 0.0396598 0.0843124 0.183797 0.0161794 0.235889 0.0154872 0.0187403 0.112429 0.0686077 0.0348512 0.0398593 0.131665 0.0667422 0.0485074 0.46866 0.258829 0.284435 0.00325504 0.0169835 +0.177941 2.0 0.00345635 0.00247935 0.0305933 0.0510623 0.0121654 0.0164915 0.00918444 0.066258 0.0152309 0.0207374 0.0100133 0.00725879 0.0464512 0.195715 0.0625971 0.142095 0.0206314 0.0383665 +0.128036 0.00116986 2.0 0.71693 0.00359188 0.144123 0.0454752 0.00382271 0.0595295 0.0146219 0.00404697 0.424466 0.0388056 0.0453065 0.0129545 0.149013 0.0457432 0.0215998 0.00373363 0.0229784 +0.274238 0.00082452 0.704411 2.0 0.00623626 0.0945269 0.0278529 0.0123487 0.320617 0.0265977 0.0122915 0.0740508 0.0624534 0.401766 0.0386212 0.0980118 0.100398 0.0834769 0.00450443 0.0138489 +0.0364693 0.0153698 0.00533148 0.00942109 2.0 0.00831369 0.0331958 0.102697 0.0110207 0.364693 0.046441 0.00751784 0.0147764 0.0073398 0.00903282 0.075904 0.0209765 0.092149 0.0440105 0.455339 +0.245455 0.0118424 0.0987547 0.065922 0.00383789 2.0 0.0121868 0.00295159 0.0463426 0.0105699 0.00679084 0.0879949 0.022293 0.0242444 0.0514178 0.186561 0.0275574 0.02655 0.00969561 0.0073091 +0.0549141 0.0096142 0.106181 0.06619 0.052219 0.0415277 2.0 0.013395 0.110465 0.0861162 0.0157637 0.309298 0.0637204 0.315429 0.18795 0.10291 0.0577555 0.0167821 0.00755458 0.273265 +0.0334964 0.00656987 0.00449938 0.0147928 0.0814349 0.00507005 0.00675232 2.0 0.0401737 0.546732 0.166064 0.0433295 0.0091461 0.00836791 0.0164437 0.0444136 0.177933 1.10899 0.00611352 0.0296423 +0.157016 0.00285886 0.0547468 0.300098 0.00682827 0.0621988 0.0435088 0.0313897 2.0 0.0444071 0.0364418 0.235475 0.0509706 0.286105 0.470625 0.134466 0.169247 0.0433079 0.00395627 0.00940156 +0.0689411 0.0148395 0.00967539 0.0179127 0.16258 0.0102073 0.024405 0.307368 0.0319516 2.0 0.189333 0.0102827 0.0380606 0.0638694 0.0437672 0.0479311 0.0398562 0.255272 0.0191421 0.0281219 +0.154803 0.0150787 0.0118373 0.0365915 0.0915163 0.0289883 0.0197474 0.412684 0.115904 0.83692 2.0 0.0154967 0.0156811 0.113509 0.06008 0.0686705 0.185005 0.29187 0.0148378 0.0302255 +0.0883341 0.010243 0.619444 0.109987 0.00739138 0.18741 0.193315 0.0537232 0.373662 0.0226778 0.00773169 2.0 0.017855 0.11339 0.0558749 0.55256 0.247719 0.027826 0.00206917 0.0766156 +0.249237 0.0042247 0.0483724 0.0792336 0.0124092 0.0405553 0.034018 0.0096863 0.069087 0.071699 0.00668276 0.0152512 2.0 0.068562 0.059757 0.224304 0.0970571 0.0446482 0.00401093 0.0152417 +0.15742 0.00381591 0.0703689 0.635103 0.00768029 0.0549548 0.209821 0.0110422 0.48319 0.149916 0.0602735 0.12068 0.085428 2.0 0.266954 0.14305 0.104689 0.042719 0.00620714 0.0160646 +0.0955629 0.0203964 0.0168059 0.0509939 0.00789476 0.0973488 0.104427 0.0181242 0.663882 0.0858074 0.026647 0.0496706 0.062191 0.222976 2.0 0.170206 0.0676525 0.03571 0.0334881 0.0269165 +0.584009 0.0543576 0.122277 0.081856 0.0419623 0.223418 0.0361666 0.030964 0.119979 0.0594392 0.019265 0.310701 0.147657 0.0755769 0.10766 2.0 0.53423 0.0330003 0.015069 0.0555211 +0.367495 0.0198092 0.0427685 0.0955377 0.0132131 0.037602 0.023127 0.141342 0.172065 0.0563155 0.0591369 0.158708 0.0727985 0.0630201 0.0487573 0.608702 2.0 0.196839 0.00318976 0.02054 +0.347553 0.0386982 0.0173799 0.0683621 0.0499532 0.0311773 0.00578328 0.758134 0.0378913 0.310411 0.0802907 0.0153423 0.0288204 0.022131 0.0221486 0.0323591 0.169399 2.0 0.0105123 0.0222037 +0.0196009 0.0276901 0.0148051 0.0181791 0.117574 0.0561089 0.0128298 0.0205964 0.0170585 0.114711 0.0201153 0.00562236 0.0127592 0.0158472 0.10236 0.0728189 0.0135282 0.0518061 2.0 0.17534 +0.0417087 0.0210004 0.0371604 0.0227943 0.4961 0.0172504 0.189266 0.0407279 0.0165324 0.0687289 0.0167114 0.0849022 0.0197739 0.0167267 0.0335535 0.10942 0.0355275 0.0446259 0.0715091 2.0 +numAuxiliaryMatrices(x>0) + 1000 +auxMatrixScaleFactor(x>=1.0) + 2.0 +numProteinTypes(x=0_then_fnaFileName,or,x>0_then_that_many_numOfProteinType_+_set_of_frequencies) + 1 +numOfProteinType[i]_(x>0,_sum_of_numOfProteinType[i=1_to_i=numProteinTypes]_>=minGenomeSize_and_<=maxGenomeSize) + 2500 +freqOf_ACDEFGHIKLMNPQRSTVWY(list_of_20_positive_values_whose_sum_is_1.0) +0.0866279 0.043972 0.0390894 0.0570451 0.0193078 0.0367281 0.0580589 0.0832518 0.0244313 0.048466 0.086209 0.0620286 0.0195027 0.0384319 0.0457631 0.0695179 0.0610127 0.0143859 0.0352742 0.0708956 diff --git a/doc/EvolSimconfigs/evolSimconfig_LGTd200.txt b/doc/EvolSimconfigs/evolSimconfig_LGTd200.txt new file mode 100755 index 0000000000000000000000000000000000000000..52484491106605ef497b8ed828a5b174f753eaac --- /dev/null +++ b/doc/EvolSimconfigs/evolSimconfig_LGTd200.txt @@ -0,0 +1,156 @@ +numIterations(x>0) + 5000 +outInterval(x>0,_may_be_>numIterations) + 5001 +rateAndBiasAdjustFrequency(x>0) + 10 +preferredMinNumLineages(x>0) + 25 +maxNumLineages(x>=preferredMinNumLineages) + 35 +speciationAndExtinctionProb(0.0<=x<1.0) + 0.5 +speciationModel{0,1,2} + 1 +selectionModel{0,1,2,3,4} + 0 +numberOfHabitats(x>=1) + 10 +numberOfHabitatNiches(x>=numberOfHabitats) + 100 +numberOfHabitatSpaces(x>=maxNumLineages_&&_x>=numberOfHabitatNiches) + 1000 +probMigrationPerIter(0.0<=x<=1.0) + 0.5 +paralogUsefulnessFactor(x>0.0) + 2.0 +meanNumLGTperIteration(x>=0.0) + 5.0 +exactPropGlobalReq(0.0<=x<=1.0) + 0.02 +meanPropHabReq(0.0<=x<=1.0) + 0.02 +meanPropNicheReq(0.0<=x<=1.0) + 0.01 + +minGenomeSize(x>0) + 2000 +maxGenomeSize(x>=minGenomeSize) + 3000 +initialTargetSize(minGenomeSize<=x<=maxGenomeSize) + 2000 +sizeAdjFactor(x>=0.0) + 1.0 +targetSizeDriftFactor(x>=0.0) + 5.0 + +duplicabilityDriftFactor(0.0<=x<=1.0) + 0.005 +inertiaDriftFactor(0.0<=x<=1.0) + 0.005 +resistanceAdjFactor(0.0<=x<=1.0) + 0.05 +selectiveDriftFactor(0.0<=x<=1.0) + 0.0005 +selectiveDriftBias(0.0<=x<=1.0) + 0.8 +maxInitialSelectivePressure(0.0<x<=1.0) + 0.2 +goodMutationProb(0.0<=x<=1.0) + 0.05 +mutationRateDriftFactor(0.0<=x<=1.0) + 0.005 +minMutationRate(0.0<x<1.0) + 0.1 +maxMutationRate(minMutationRate<=x<1.0) + 0.1 +mutationRate(0.0<x<1.0) + 0.1 +transitionProbDriftFactor(0.0<=x<=1.0) + 0.0005 +minTransitionProb(0.0<x<1.0) + 0.5 +maxTransitionProb(minTransitionProb<=x<1.0) + 0.9 +transitionProb(0.0<x<1.0) + 0.666667 +gcBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minGCbias(0.0<x<1.0) + 0.25 +maxGCbias(minGCbias<=x<1.0) + 0.75 +gcBias(0.0<x<1.0) + 0.5 +purineBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minPurineBias(0.0<x<1.0) + 0.1 +maxPurineBias(minPurineBias<=x<1.0) + 0.25 +purineBias(0.0<x<1.0) + 0.1 + +randomLGTProb(0.0<=x<=1.0) + 0.0 +divergenceLGTProb(0.0<=x<=1.0) + 1.0 +geneCompLGTProb(0.0<=x<=1.0) + 0.0 +gcLGTProb(0.0<=x<=1.0) + 0.0 +habitatLGTProb(0.0<=x<=1.0) + 0.0 + +divergenceFactor(x>0.0,_normally_x<=numIterations) + 200.0 +geneCompSimilarityFactor(0.0<=x<1.0) + 0.9 +gcSimilarityFactor(0.0<x<=1.0) + 0.9 +orthologReplacementProbability(0.0<=x<=1.0) + 1.0 +lgtReceptivityDriftFactor(0.0<=x<=1.0) + 0.005 +lgtMinReceptivity(0.0<=x<=1.0) + 1.0 +lgtMaxReceptivity(lgtMinReceptivity<=x<=1.0) + 1.0 +lgtReceptivity(0<=x<=1.0) + 1.0 + +minGeneSize(x>0) + 80 +maxGeneSize(x>=minGeneSize) + 500 +substitutionMatrix(list_of_400_positive_values_<=2.0,_ACDEFGHIKLMNPQRSTVWY_x_ACDEFGHIKLMNPQRSTVWY) +2.0 0.0396598 0.0843124 0.183797 0.0161794 0.235889 0.0154872 0.0187403 0.112429 0.0686077 0.0348512 0.0398593 0.131665 0.0667422 0.0485074 0.46866 0.258829 0.284435 0.00325504 0.0169835 +0.177941 2.0 0.00345635 0.00247935 0.0305933 0.0510623 0.0121654 0.0164915 0.00918444 0.066258 0.0152309 0.0207374 0.0100133 0.00725879 0.0464512 0.195715 0.0625971 0.142095 0.0206314 0.0383665 +0.128036 0.00116986 2.0 0.71693 0.00359188 0.144123 0.0454752 0.00382271 0.0595295 0.0146219 0.00404697 0.424466 0.0388056 0.0453065 0.0129545 0.149013 0.0457432 0.0215998 0.00373363 0.0229784 +0.274238 0.00082452 0.704411 2.0 0.00623626 0.0945269 0.0278529 0.0123487 0.320617 0.0265977 0.0122915 0.0740508 0.0624534 0.401766 0.0386212 0.0980118 0.100398 0.0834769 0.00450443 0.0138489 +0.0364693 0.0153698 0.00533148 0.00942109 2.0 0.00831369 0.0331958 0.102697 0.0110207 0.364693 0.046441 0.00751784 0.0147764 0.0073398 0.00903282 0.075904 0.0209765 0.092149 0.0440105 0.455339 +0.245455 0.0118424 0.0987547 0.065922 0.00383789 2.0 0.0121868 0.00295159 0.0463426 0.0105699 0.00679084 0.0879949 0.022293 0.0242444 0.0514178 0.186561 0.0275574 0.02655 0.00969561 0.0073091 +0.0549141 0.0096142 0.106181 0.06619 0.052219 0.0415277 2.0 0.013395 0.110465 0.0861162 0.0157637 0.309298 0.0637204 0.315429 0.18795 0.10291 0.0577555 0.0167821 0.00755458 0.273265 +0.0334964 0.00656987 0.00449938 0.0147928 0.0814349 0.00507005 0.00675232 2.0 0.0401737 0.546732 0.166064 0.0433295 0.0091461 0.00836791 0.0164437 0.0444136 0.177933 1.10899 0.00611352 0.0296423 +0.157016 0.00285886 0.0547468 0.300098 0.00682827 0.0621988 0.0435088 0.0313897 2.0 0.0444071 0.0364418 0.235475 0.0509706 0.286105 0.470625 0.134466 0.169247 0.0433079 0.00395627 0.00940156 +0.0689411 0.0148395 0.00967539 0.0179127 0.16258 0.0102073 0.024405 0.307368 0.0319516 2.0 0.189333 0.0102827 0.0380606 0.0638694 0.0437672 0.0479311 0.0398562 0.255272 0.0191421 0.0281219 +0.154803 0.0150787 0.0118373 0.0365915 0.0915163 0.0289883 0.0197474 0.412684 0.115904 0.83692 2.0 0.0154967 0.0156811 0.113509 0.06008 0.0686705 0.185005 0.29187 0.0148378 0.0302255 +0.0883341 0.010243 0.619444 0.109987 0.00739138 0.18741 0.193315 0.0537232 0.373662 0.0226778 0.00773169 2.0 0.017855 0.11339 0.0558749 0.55256 0.247719 0.027826 0.00206917 0.0766156 +0.249237 0.0042247 0.0483724 0.0792336 0.0124092 0.0405553 0.034018 0.0096863 0.069087 0.071699 0.00668276 0.0152512 2.0 0.068562 0.059757 0.224304 0.0970571 0.0446482 0.00401093 0.0152417 +0.15742 0.00381591 0.0703689 0.635103 0.00768029 0.0549548 0.209821 0.0110422 0.48319 0.149916 0.0602735 0.12068 0.085428 2.0 0.266954 0.14305 0.104689 0.042719 0.00620714 0.0160646 +0.0955629 0.0203964 0.0168059 0.0509939 0.00789476 0.0973488 0.104427 0.0181242 0.663882 0.0858074 0.026647 0.0496706 0.062191 0.222976 2.0 0.170206 0.0676525 0.03571 0.0334881 0.0269165 +0.584009 0.0543576 0.122277 0.081856 0.0419623 0.223418 0.0361666 0.030964 0.119979 0.0594392 0.019265 0.310701 0.147657 0.0755769 0.10766 2.0 0.53423 0.0330003 0.015069 0.0555211 +0.367495 0.0198092 0.0427685 0.0955377 0.0132131 0.037602 0.023127 0.141342 0.172065 0.0563155 0.0591369 0.158708 0.0727985 0.0630201 0.0487573 0.608702 2.0 0.196839 0.00318976 0.02054 +0.347553 0.0386982 0.0173799 0.0683621 0.0499532 0.0311773 0.00578328 0.758134 0.0378913 0.310411 0.0802907 0.0153423 0.0288204 0.022131 0.0221486 0.0323591 0.169399 2.0 0.0105123 0.0222037 +0.0196009 0.0276901 0.0148051 0.0181791 0.117574 0.0561089 0.0128298 0.0205964 0.0170585 0.114711 0.0201153 0.00562236 0.0127592 0.0158472 0.10236 0.0728189 0.0135282 0.0518061 2.0 0.17534 +0.0417087 0.0210004 0.0371604 0.0227943 0.4961 0.0172504 0.189266 0.0407279 0.0165324 0.0687289 0.0167114 0.0849022 0.0197739 0.0167267 0.0335535 0.10942 0.0355275 0.0446259 0.0715091 2.0 +numAuxiliaryMatrices(x>0) + 1000 +auxMatrixScaleFactor(x>=1.0) + 2.0 +numProteinTypes(x=0_then_fnaFileName,or,x>0_then_that_many_numOfProteinType_+_set_of_frequencies) + 1 +numOfProteinType[i]_(x>0,_sum_of_numOfProteinType[i=1_to_i=numProteinTypes]_>=minGenomeSize_and_<=maxGenomeSize) + 2500 +freqOf_ACDEFGHIKLMNPQRSTVWY(list_of_20_positive_values_whose_sum_is_1.0) +0.0866279 0.043972 0.0390894 0.0570451 0.0193078 0.0367281 0.0580589 0.0832518 0.0244313 0.048466 0.086209 0.0620286 0.0195027 0.0384319 0.0457631 0.0695179 0.0610127 0.0143859 0.0352742 0.0708956 diff --git a/doc/EvolSimconfigs/evolSimconfig_LGTd3000.txt b/doc/EvolSimconfigs/evolSimconfig_LGTd3000.txt new file mode 100755 index 0000000000000000000000000000000000000000..a807154785804cdadf6b352248433e5fa516ea18 --- /dev/null +++ b/doc/EvolSimconfigs/evolSimconfig_LGTd3000.txt @@ -0,0 +1,156 @@ +numIterations(x>0) + 5000 +outInterval(x>0,_may_be_>numIterations) + 5001 +rateAndBiasAdjustFrequency(x>0) + 10 +preferredMinNumLineages(x>0) + 25 +maxNumLineages(x>=preferredMinNumLineages) + 35 +speciationAndExtinctionProb(0.0<=x<1.0) + 0.5 +speciationModel{0,1,2} + 1 +selectionModel{0,1,2,3,4} + 0 +numberOfHabitats(x>=1) + 10 +numberOfHabitatNiches(x>=numberOfHabitats) + 100 +numberOfHabitatSpaces(x>=maxNumLineages_&&_x>=numberOfHabitatNiches) + 1000 +probMigrationPerIter(0.0<=x<=1.0) + 0.5 +paralogUsefulnessFactor(x>0.0) + 2.0 +meanNumLGTperIteration(x>=0.0) + 5.0 +exactPropGlobalReq(0.0<=x<=1.0) + 0.02 +meanPropHabReq(0.0<=x<=1.0) + 0.02 +meanPropNicheReq(0.0<=x<=1.0) + 0.01 + +minGenomeSize(x>0) + 2000 +maxGenomeSize(x>=minGenomeSize) + 3000 +initialTargetSize(minGenomeSize<=x<=maxGenomeSize) + 2000 +sizeAdjFactor(x>=0.0) + 1.0 +targetSizeDriftFactor(x>=0.0) + 5.0 + +duplicabilityDriftFactor(0.0<=x<=1.0) + 0.005 +inertiaDriftFactor(0.0<=x<=1.0) + 0.005 +resistanceAdjFactor(0.0<=x<=1.0) + 0.05 +selectiveDriftFactor(0.0<=x<=1.0) + 0.0005 +selectiveDriftBias(0.0<=x<=1.0) + 0.8 +maxInitialSelectivePressure(0.0<x<=1.0) + 0.2 +goodMutationProb(0.0<=x<=1.0) + 0.05 +mutationRateDriftFactor(0.0<=x<=1.0) + 0.005 +minMutationRate(0.0<x<1.0) + 0.1 +maxMutationRate(minMutationRate<=x<1.0) + 0.1 +mutationRate(0.0<x<1.0) + 0.1 +transitionProbDriftFactor(0.0<=x<=1.0) + 0.0005 +minTransitionProb(0.0<x<1.0) + 0.5 +maxTransitionProb(minTransitionProb<=x<1.0) + 0.9 +transitionProb(0.0<x<1.0) + 0.666667 +gcBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minGCbias(0.0<x<1.0) + 0.25 +maxGCbias(minGCbias<=x<1.0) + 0.75 +gcBias(0.0<x<1.0) + 0.5 +purineBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minPurineBias(0.0<x<1.0) + 0.1 +maxPurineBias(minPurineBias<=x<1.0) + 0.25 +purineBias(0.0<x<1.0) + 0.1 + +randomLGTProb(0.0<=x<=1.0) + 0.0 +divergenceLGTProb(0.0<=x<=1.0) + 1.0 +geneCompLGTProb(0.0<=x<=1.0) + 0.0 +gcLGTProb(0.0<=x<=1.0) + 0.0 +habitatLGTProb(0.0<=x<=1.0) + 0.0 + +divergenceFactor(x>0.0,_normally_x<=numIterations) + 3000.0 +geneCompSimilarityFactor(0.0<=x<1.0) + 0.9 +gcSimilarityFactor(0.0<x<=1.0) + 0.9 +orthologReplacementProbability(0.0<=x<=1.0) + 1.0 +lgtReceptivityDriftFactor(0.0<=x<=1.0) + 0.005 +lgtMinReceptivity(0.0<=x<=1.0) + 1.0 +lgtMaxReceptivity(lgtMinReceptivity<=x<=1.0) + 1.0 +lgtReceptivity(0<=x<=1.0) + 1.0 + +minGeneSize(x>0) + 80 +maxGeneSize(x>=minGeneSize) + 500 +substitutionMatrix(list_of_400_positive_values_<=2.0,_ACDEFGHIKLMNPQRSTVWY_x_ACDEFGHIKLMNPQRSTVWY) +2.0 0.0396598 0.0843124 0.183797 0.0161794 0.235889 0.0154872 0.0187403 0.112429 0.0686077 0.0348512 0.0398593 0.131665 0.0667422 0.0485074 0.46866 0.258829 0.284435 0.00325504 0.0169835 +0.177941 2.0 0.00345635 0.00247935 0.0305933 0.0510623 0.0121654 0.0164915 0.00918444 0.066258 0.0152309 0.0207374 0.0100133 0.00725879 0.0464512 0.195715 0.0625971 0.142095 0.0206314 0.0383665 +0.128036 0.00116986 2.0 0.71693 0.00359188 0.144123 0.0454752 0.00382271 0.0595295 0.0146219 0.00404697 0.424466 0.0388056 0.0453065 0.0129545 0.149013 0.0457432 0.0215998 0.00373363 0.0229784 +0.274238 0.00082452 0.704411 2.0 0.00623626 0.0945269 0.0278529 0.0123487 0.320617 0.0265977 0.0122915 0.0740508 0.0624534 0.401766 0.0386212 0.0980118 0.100398 0.0834769 0.00450443 0.0138489 +0.0364693 0.0153698 0.00533148 0.00942109 2.0 0.00831369 0.0331958 0.102697 0.0110207 0.364693 0.046441 0.00751784 0.0147764 0.0073398 0.00903282 0.075904 0.0209765 0.092149 0.0440105 0.455339 +0.245455 0.0118424 0.0987547 0.065922 0.00383789 2.0 0.0121868 0.00295159 0.0463426 0.0105699 0.00679084 0.0879949 0.022293 0.0242444 0.0514178 0.186561 0.0275574 0.02655 0.00969561 0.0073091 +0.0549141 0.0096142 0.106181 0.06619 0.052219 0.0415277 2.0 0.013395 0.110465 0.0861162 0.0157637 0.309298 0.0637204 0.315429 0.18795 0.10291 0.0577555 0.0167821 0.00755458 0.273265 +0.0334964 0.00656987 0.00449938 0.0147928 0.0814349 0.00507005 0.00675232 2.0 0.0401737 0.546732 0.166064 0.0433295 0.0091461 0.00836791 0.0164437 0.0444136 0.177933 1.10899 0.00611352 0.0296423 +0.157016 0.00285886 0.0547468 0.300098 0.00682827 0.0621988 0.0435088 0.0313897 2.0 0.0444071 0.0364418 0.235475 0.0509706 0.286105 0.470625 0.134466 0.169247 0.0433079 0.00395627 0.00940156 +0.0689411 0.0148395 0.00967539 0.0179127 0.16258 0.0102073 0.024405 0.307368 0.0319516 2.0 0.189333 0.0102827 0.0380606 0.0638694 0.0437672 0.0479311 0.0398562 0.255272 0.0191421 0.0281219 +0.154803 0.0150787 0.0118373 0.0365915 0.0915163 0.0289883 0.0197474 0.412684 0.115904 0.83692 2.0 0.0154967 0.0156811 0.113509 0.06008 0.0686705 0.185005 0.29187 0.0148378 0.0302255 +0.0883341 0.010243 0.619444 0.109987 0.00739138 0.18741 0.193315 0.0537232 0.373662 0.0226778 0.00773169 2.0 0.017855 0.11339 0.0558749 0.55256 0.247719 0.027826 0.00206917 0.0766156 +0.249237 0.0042247 0.0483724 0.0792336 0.0124092 0.0405553 0.034018 0.0096863 0.069087 0.071699 0.00668276 0.0152512 2.0 0.068562 0.059757 0.224304 0.0970571 0.0446482 0.00401093 0.0152417 +0.15742 0.00381591 0.0703689 0.635103 0.00768029 0.0549548 0.209821 0.0110422 0.48319 0.149916 0.0602735 0.12068 0.085428 2.0 0.266954 0.14305 0.104689 0.042719 0.00620714 0.0160646 +0.0955629 0.0203964 0.0168059 0.0509939 0.00789476 0.0973488 0.104427 0.0181242 0.663882 0.0858074 0.026647 0.0496706 0.062191 0.222976 2.0 0.170206 0.0676525 0.03571 0.0334881 0.0269165 +0.584009 0.0543576 0.122277 0.081856 0.0419623 0.223418 0.0361666 0.030964 0.119979 0.0594392 0.019265 0.310701 0.147657 0.0755769 0.10766 2.0 0.53423 0.0330003 0.015069 0.0555211 +0.367495 0.0198092 0.0427685 0.0955377 0.0132131 0.037602 0.023127 0.141342 0.172065 0.0563155 0.0591369 0.158708 0.0727985 0.0630201 0.0487573 0.608702 2.0 0.196839 0.00318976 0.02054 +0.347553 0.0386982 0.0173799 0.0683621 0.0499532 0.0311773 0.00578328 0.758134 0.0378913 0.310411 0.0802907 0.0153423 0.0288204 0.022131 0.0221486 0.0323591 0.169399 2.0 0.0105123 0.0222037 +0.0196009 0.0276901 0.0148051 0.0181791 0.117574 0.0561089 0.0128298 0.0205964 0.0170585 0.114711 0.0201153 0.00562236 0.0127592 0.0158472 0.10236 0.0728189 0.0135282 0.0518061 2.0 0.17534 +0.0417087 0.0210004 0.0371604 0.0227943 0.4961 0.0172504 0.189266 0.0407279 0.0165324 0.0687289 0.0167114 0.0849022 0.0197739 0.0167267 0.0335535 0.10942 0.0355275 0.0446259 0.0715091 2.0 +numAuxiliaryMatrices(x>0) + 1000 +auxMatrixScaleFactor(x>=1.0) + 2.0 +numProteinTypes(x=0_then_fnaFileName,or,x>0_then_that_many_numOfProteinType_+_set_of_frequencies) + 1 +numOfProteinType[i]_(x>0,_sum_of_numOfProteinType[i=1_to_i=numProteinTypes]_>=minGenomeSize_and_<=maxGenomeSize) + 2500 +freqOf_ACDEFGHIKLMNPQRSTVWY(list_of_20_positive_values_whose_sum_is_1.0) +0.0866279 0.043972 0.0390894 0.0570451 0.0193078 0.0367281 0.0580589 0.0832518 0.0244313 0.048466 0.086209 0.0620286 0.0195027 0.0384319 0.0457631 0.0695179 0.0610127 0.0143859 0.0352742 0.0708956 diff --git a/doc/EvolSimconfigs/evolSimconfig_LGTd5000.txt b/doc/EvolSimconfigs/evolSimconfig_LGTd5000.txt new file mode 100755 index 0000000000000000000000000000000000000000..f67e808631ca02eda01fc1508555cb1575dfb927 --- /dev/null +++ b/doc/EvolSimconfigs/evolSimconfig_LGTd5000.txt @@ -0,0 +1,156 @@ +numIterations(x>0) + 5000 +outInterval(x>0,_may_be_>numIterations) + 5001 +rateAndBiasAdjustFrequency(x>0) + 10 +preferredMinNumLineages(x>0) + 25 +maxNumLineages(x>=preferredMinNumLineages) + 35 +speciationAndExtinctionProb(0.0<=x<1.0) + 0.5 +speciationModel{0,1,2} + 1 +selectionModel{0,1,2,3,4} + 0 +numberOfHabitats(x>=1) + 10 +numberOfHabitatNiches(x>=numberOfHabitats) + 100 +numberOfHabitatSpaces(x>=maxNumLineages_&&_x>=numberOfHabitatNiches) + 1000 +probMigrationPerIter(0.0<=x<=1.0) + 0.5 +paralogUsefulnessFactor(x>0.0) + 2.0 +meanNumLGTperIteration(x>=0.0) + 5.0 +exactPropGlobalReq(0.0<=x<=1.0) + 0.02 +meanPropHabReq(0.0<=x<=1.0) + 0.02 +meanPropNicheReq(0.0<=x<=1.0) + 0.01 + +minGenomeSize(x>0) + 2000 +maxGenomeSize(x>=minGenomeSize) + 3000 +initialTargetSize(minGenomeSize<=x<=maxGenomeSize) + 2000 +sizeAdjFactor(x>=0.0) + 1.0 +targetSizeDriftFactor(x>=0.0) + 5.0 + +duplicabilityDriftFactor(0.0<=x<=1.0) + 0.005 +inertiaDriftFactor(0.0<=x<=1.0) + 0.005 +resistanceAdjFactor(0.0<=x<=1.0) + 0.05 +selectiveDriftFactor(0.0<=x<=1.0) + 0.0005 +selectiveDriftBias(0.0<=x<=1.0) + 0.8 +maxInitialSelectivePressure(0.0<x<=1.0) + 0.2 +goodMutationProb(0.0<=x<=1.0) + 0.05 +mutationRateDriftFactor(0.0<=x<=1.0) + 0.005 +minMutationRate(0.0<x<1.0) + 0.1 +maxMutationRate(minMutationRate<=x<1.0) + 0.1 +mutationRate(0.0<x<1.0) + 0.1 +transitionProbDriftFactor(0.0<=x<=1.0) + 0.0005 +minTransitionProb(0.0<x<1.0) + 0.5 +maxTransitionProb(minTransitionProb<=x<1.0) + 0.9 +transitionProb(0.0<x<1.0) + 0.666667 +gcBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minGCbias(0.0<x<1.0) + 0.25 +maxGCbias(minGCbias<=x<1.0) + 0.75 +gcBias(0.0<x<1.0) + 0.5 +purineBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minPurineBias(0.0<x<1.0) + 0.1 +maxPurineBias(minPurineBias<=x<1.0) + 0.25 +purineBias(0.0<x<1.0) + 0.1 + +randomLGTProb(0.0<=x<=1.0) + 0.0 +divergenceLGTProb(0.0<=x<=1.0) + 1.0 +geneCompLGTProb(0.0<=x<=1.0) + 0.0 +gcLGTProb(0.0<=x<=1.0) + 0.0 +habitatLGTProb(0.0<=x<=1.0) + 0.0 + +divergenceFactor(x>0.0,_normally_x<=numIterations) + 5000.0 +geneCompSimilarityFactor(0.0<=x<1.0) + 0.9 +gcSimilarityFactor(0.0<x<=1.0) + 0.9 +orthologReplacementProbability(0.0<=x<=1.0) + 1.0 +lgtReceptivityDriftFactor(0.0<=x<=1.0) + 0.005 +lgtMinReceptivity(0.0<=x<=1.0) + 1.0 +lgtMaxReceptivity(lgtMinReceptivity<=x<=1.0) + 1.0 +lgtReceptivity(0<=x<=1.0) + 1.0 + +minGeneSize(x>0) + 80 +maxGeneSize(x>=minGeneSize) + 500 +substitutionMatrix(list_of_400_positive_values_<=2.0,_ACDEFGHIKLMNPQRSTVWY_x_ACDEFGHIKLMNPQRSTVWY) +2.0 0.0396598 0.0843124 0.183797 0.0161794 0.235889 0.0154872 0.0187403 0.112429 0.0686077 0.0348512 0.0398593 0.131665 0.0667422 0.0485074 0.46866 0.258829 0.284435 0.00325504 0.0169835 +0.177941 2.0 0.00345635 0.00247935 0.0305933 0.0510623 0.0121654 0.0164915 0.00918444 0.066258 0.0152309 0.0207374 0.0100133 0.00725879 0.0464512 0.195715 0.0625971 0.142095 0.0206314 0.0383665 +0.128036 0.00116986 2.0 0.71693 0.00359188 0.144123 0.0454752 0.00382271 0.0595295 0.0146219 0.00404697 0.424466 0.0388056 0.0453065 0.0129545 0.149013 0.0457432 0.0215998 0.00373363 0.0229784 +0.274238 0.00082452 0.704411 2.0 0.00623626 0.0945269 0.0278529 0.0123487 0.320617 0.0265977 0.0122915 0.0740508 0.0624534 0.401766 0.0386212 0.0980118 0.100398 0.0834769 0.00450443 0.0138489 +0.0364693 0.0153698 0.00533148 0.00942109 2.0 0.00831369 0.0331958 0.102697 0.0110207 0.364693 0.046441 0.00751784 0.0147764 0.0073398 0.00903282 0.075904 0.0209765 0.092149 0.0440105 0.455339 +0.245455 0.0118424 0.0987547 0.065922 0.00383789 2.0 0.0121868 0.00295159 0.0463426 0.0105699 0.00679084 0.0879949 0.022293 0.0242444 0.0514178 0.186561 0.0275574 0.02655 0.00969561 0.0073091 +0.0549141 0.0096142 0.106181 0.06619 0.052219 0.0415277 2.0 0.013395 0.110465 0.0861162 0.0157637 0.309298 0.0637204 0.315429 0.18795 0.10291 0.0577555 0.0167821 0.00755458 0.273265 +0.0334964 0.00656987 0.00449938 0.0147928 0.0814349 0.00507005 0.00675232 2.0 0.0401737 0.546732 0.166064 0.0433295 0.0091461 0.00836791 0.0164437 0.0444136 0.177933 1.10899 0.00611352 0.0296423 +0.157016 0.00285886 0.0547468 0.300098 0.00682827 0.0621988 0.0435088 0.0313897 2.0 0.0444071 0.0364418 0.235475 0.0509706 0.286105 0.470625 0.134466 0.169247 0.0433079 0.00395627 0.00940156 +0.0689411 0.0148395 0.00967539 0.0179127 0.16258 0.0102073 0.024405 0.307368 0.0319516 2.0 0.189333 0.0102827 0.0380606 0.0638694 0.0437672 0.0479311 0.0398562 0.255272 0.0191421 0.0281219 +0.154803 0.0150787 0.0118373 0.0365915 0.0915163 0.0289883 0.0197474 0.412684 0.115904 0.83692 2.0 0.0154967 0.0156811 0.113509 0.06008 0.0686705 0.185005 0.29187 0.0148378 0.0302255 +0.0883341 0.010243 0.619444 0.109987 0.00739138 0.18741 0.193315 0.0537232 0.373662 0.0226778 0.00773169 2.0 0.017855 0.11339 0.0558749 0.55256 0.247719 0.027826 0.00206917 0.0766156 +0.249237 0.0042247 0.0483724 0.0792336 0.0124092 0.0405553 0.034018 0.0096863 0.069087 0.071699 0.00668276 0.0152512 2.0 0.068562 0.059757 0.224304 0.0970571 0.0446482 0.00401093 0.0152417 +0.15742 0.00381591 0.0703689 0.635103 0.00768029 0.0549548 0.209821 0.0110422 0.48319 0.149916 0.0602735 0.12068 0.085428 2.0 0.266954 0.14305 0.104689 0.042719 0.00620714 0.0160646 +0.0955629 0.0203964 0.0168059 0.0509939 0.00789476 0.0973488 0.104427 0.0181242 0.663882 0.0858074 0.026647 0.0496706 0.062191 0.222976 2.0 0.170206 0.0676525 0.03571 0.0334881 0.0269165 +0.584009 0.0543576 0.122277 0.081856 0.0419623 0.223418 0.0361666 0.030964 0.119979 0.0594392 0.019265 0.310701 0.147657 0.0755769 0.10766 2.0 0.53423 0.0330003 0.015069 0.0555211 +0.367495 0.0198092 0.0427685 0.0955377 0.0132131 0.037602 0.023127 0.141342 0.172065 0.0563155 0.0591369 0.158708 0.0727985 0.0630201 0.0487573 0.608702 2.0 0.196839 0.00318976 0.02054 +0.347553 0.0386982 0.0173799 0.0683621 0.0499532 0.0311773 0.00578328 0.758134 0.0378913 0.310411 0.0802907 0.0153423 0.0288204 0.022131 0.0221486 0.0323591 0.169399 2.0 0.0105123 0.0222037 +0.0196009 0.0276901 0.0148051 0.0181791 0.117574 0.0561089 0.0128298 0.0205964 0.0170585 0.114711 0.0201153 0.00562236 0.0127592 0.0158472 0.10236 0.0728189 0.0135282 0.0518061 2.0 0.17534 +0.0417087 0.0210004 0.0371604 0.0227943 0.4961 0.0172504 0.189266 0.0407279 0.0165324 0.0687289 0.0167114 0.0849022 0.0197739 0.0167267 0.0335535 0.10942 0.0355275 0.0446259 0.0715091 2.0 +numAuxiliaryMatrices(x>0) + 1000 +auxMatrixScaleFactor(x>=1.0) + 2.0 +numProteinTypes(x=0_then_fnaFileName,or,x>0_then_that_many_numOfProteinType_+_set_of_frequencies) + 1 +numOfProteinType[i]_(x>0,_sum_of_numOfProteinType[i=1_to_i=numProteinTypes]_>=minGenomeSize_and_<=maxGenomeSize) + 2500 +freqOf_ACDEFGHIKLMNPQRSTVWY(list_of_20_positive_values_whose_sum_is_1.0) +0.0866279 0.043972 0.0390894 0.0570451 0.0193078 0.0367281 0.0580589 0.0832518 0.0244313 0.048466 0.086209 0.0620286 0.0195027 0.0384319 0.0457631 0.0695179 0.0610127 0.0143859 0.0352742 0.0708956 diff --git a/doc/EvolSimconfigs/evolSimconfig_LGTl125.txt b/doc/EvolSimconfigs/evolSimconfig_LGTl125.txt new file mode 100755 index 0000000000000000000000000000000000000000..423542cc497c11f6c598c6b1fe689ef8fe2d3bdc --- /dev/null +++ b/doc/EvolSimconfigs/evolSimconfig_LGTl125.txt @@ -0,0 +1,156 @@ +numIterations(x>0) + 5000 +outInterval(x>0,_may_be_>numIterations) + 5001 +rateAndBiasAdjustFrequency(x>0) + 10 +preferredMinNumLineages(x>0) + 25 +maxNumLineages(x>=preferredMinNumLineages) + 35 +speciationAndExtinctionProb(0.0<=x<1.0) + 0.5 +speciationModel{0,1,2} + 1 +selectionModel{0,1,2,3,4} + 0 +numberOfHabitats(x>=1) + 10 +numberOfHabitatNiches(x>=numberOfHabitats) + 100 +numberOfHabitatSpaces(x>=maxNumLineages_&&_x>=numberOfHabitatNiches) + 1000 +probMigrationPerIter(0.0<=x<=1.0) + 0.5 +paralogUsefulnessFactor(x>0.0) + 2.0 +meanNumLGTperIteration(x>=0.0) + 125.0 +exactPropGlobalReq(0.0<=x<=1.0) + 0.02 +meanPropHabReq(0.0<=x<=1.0) + 0.02 +meanPropNicheReq(0.0<=x<=1.0) + 0.01 + +minGenomeSize(x>0) + 2000 +maxGenomeSize(x>=minGenomeSize) + 3000 +initialTargetSize(minGenomeSize<=x<=maxGenomeSize) + 2000 +sizeAdjFactor(x>=0.0) + 1.0 +targetSizeDriftFactor(x>=0.0) + 5.0 + +duplicabilityDriftFactor(0.0<=x<=1.0) + 0.005 +inertiaDriftFactor(0.0<=x<=1.0) + 0.005 +resistanceAdjFactor(0.0<=x<=1.0) + 0.05 +selectiveDriftFactor(0.0<=x<=1.0) + 0.0005 +selectiveDriftBias(0.0<=x<=1.0) + 0.8 +maxInitialSelectivePressure(0.0<x<=1.0) + 0.2 +goodMutationProb(0.0<=x<=1.0) + 0.05 +mutationRateDriftFactor(0.0<=x<=1.0) + 0.005 +minMutationRate(0.0<x<1.0) + 0.1 +maxMutationRate(minMutationRate<=x<1.0) + 0.1 +mutationRate(0.0<x<1.0) + 0.1 +transitionProbDriftFactor(0.0<=x<=1.0) + 0.0005 +minTransitionProb(0.0<x<1.0) + 0.5 +maxTransitionProb(minTransitionProb<=x<1.0) + 0.9 +transitionProb(0.0<x<1.0) + 0.666667 +gcBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minGCbias(0.0<x<1.0) + 0.25 +maxGCbias(minGCbias<=x<1.0) + 0.75 +gcBias(0.0<x<1.0) + 0.5 +purineBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minPurineBias(0.0<x<1.0) + 0.1 +maxPurineBias(minPurineBias<=x<1.0) + 0.25 +purineBias(0.0<x<1.0) + 0.1 + +randomLGTProb(0.0<=x<=1.0) + 1.0 +divergenceLGTProb(0.0<=x<=1.0) + 0.0 +geneCompLGTProb(0.0<=x<=1.0) + 0.0 +gcLGTProb(0.0<=x<=1.0) + 0.0 +habitatLGTProb(0.0<=x<=1.0) + 0.0 + +divergenceFactor(x>0.0,_normally_x<=numIterations) + 5000.0 +geneCompSimilarityFactor(0.0<=x<1.0) + 0.9 +gcSimilarityFactor(0.0<x<=1.0) + 0.9 +orthologReplacementProbability(0.0<=x<=1.0) + 1.0 +lgtReceptivityDriftFactor(0.0<=x<=1.0) + 0.005 +lgtMinReceptivity(0.0<=x<=1.0) + 1.0 +lgtMaxReceptivity(lgtMinReceptivity<=x<=1.0) + 1.0 +lgtReceptivity(0<=x<=1.0) + 1.0 + +minGeneSize(x>0) + 80 +maxGeneSize(x>=minGeneSize) + 500 +substitutionMatrix(list_of_400_positive_values_<=2.0,_ACDEFGHIKLMNPQRSTVWY_x_ACDEFGHIKLMNPQRSTVWY) +2.0 0.0396598 0.0843124 0.183797 0.0161794 0.235889 0.0154872 0.0187403 0.112429 0.0686077 0.0348512 0.0398593 0.131665 0.0667422 0.0485074 0.46866 0.258829 0.284435 0.00325504 0.0169835 +0.177941 2.0 0.00345635 0.00247935 0.0305933 0.0510623 0.0121654 0.0164915 0.00918444 0.066258 0.0152309 0.0207374 0.0100133 0.00725879 0.0464512 0.195715 0.0625971 0.142095 0.0206314 0.0383665 +0.128036 0.00116986 2.0 0.71693 0.00359188 0.144123 0.0454752 0.00382271 0.0595295 0.0146219 0.00404697 0.424466 0.0388056 0.0453065 0.0129545 0.149013 0.0457432 0.0215998 0.00373363 0.0229784 +0.274238 0.00082452 0.704411 2.0 0.00623626 0.0945269 0.0278529 0.0123487 0.320617 0.0265977 0.0122915 0.0740508 0.0624534 0.401766 0.0386212 0.0980118 0.100398 0.0834769 0.00450443 0.0138489 +0.0364693 0.0153698 0.00533148 0.00942109 2.0 0.00831369 0.0331958 0.102697 0.0110207 0.364693 0.046441 0.00751784 0.0147764 0.0073398 0.00903282 0.075904 0.0209765 0.092149 0.0440105 0.455339 +0.245455 0.0118424 0.0987547 0.065922 0.00383789 2.0 0.0121868 0.00295159 0.0463426 0.0105699 0.00679084 0.0879949 0.022293 0.0242444 0.0514178 0.186561 0.0275574 0.02655 0.00969561 0.0073091 +0.0549141 0.0096142 0.106181 0.06619 0.052219 0.0415277 2.0 0.013395 0.110465 0.0861162 0.0157637 0.309298 0.0637204 0.315429 0.18795 0.10291 0.0577555 0.0167821 0.00755458 0.273265 +0.0334964 0.00656987 0.00449938 0.0147928 0.0814349 0.00507005 0.00675232 2.0 0.0401737 0.546732 0.166064 0.0433295 0.0091461 0.00836791 0.0164437 0.0444136 0.177933 1.10899 0.00611352 0.0296423 +0.157016 0.00285886 0.0547468 0.300098 0.00682827 0.0621988 0.0435088 0.0313897 2.0 0.0444071 0.0364418 0.235475 0.0509706 0.286105 0.470625 0.134466 0.169247 0.0433079 0.00395627 0.00940156 +0.0689411 0.0148395 0.00967539 0.0179127 0.16258 0.0102073 0.024405 0.307368 0.0319516 2.0 0.189333 0.0102827 0.0380606 0.0638694 0.0437672 0.0479311 0.0398562 0.255272 0.0191421 0.0281219 +0.154803 0.0150787 0.0118373 0.0365915 0.0915163 0.0289883 0.0197474 0.412684 0.115904 0.83692 2.0 0.0154967 0.0156811 0.113509 0.06008 0.0686705 0.185005 0.29187 0.0148378 0.0302255 +0.0883341 0.010243 0.619444 0.109987 0.00739138 0.18741 0.193315 0.0537232 0.373662 0.0226778 0.00773169 2.0 0.017855 0.11339 0.0558749 0.55256 0.247719 0.027826 0.00206917 0.0766156 +0.249237 0.0042247 0.0483724 0.0792336 0.0124092 0.0405553 0.034018 0.0096863 0.069087 0.071699 0.00668276 0.0152512 2.0 0.068562 0.059757 0.224304 0.0970571 0.0446482 0.00401093 0.0152417 +0.15742 0.00381591 0.0703689 0.635103 0.00768029 0.0549548 0.209821 0.0110422 0.48319 0.149916 0.0602735 0.12068 0.085428 2.0 0.266954 0.14305 0.104689 0.042719 0.00620714 0.0160646 +0.0955629 0.0203964 0.0168059 0.0509939 0.00789476 0.0973488 0.104427 0.0181242 0.663882 0.0858074 0.026647 0.0496706 0.062191 0.222976 2.0 0.170206 0.0676525 0.03571 0.0334881 0.0269165 +0.584009 0.0543576 0.122277 0.081856 0.0419623 0.223418 0.0361666 0.030964 0.119979 0.0594392 0.019265 0.310701 0.147657 0.0755769 0.10766 2.0 0.53423 0.0330003 0.015069 0.0555211 +0.367495 0.0198092 0.0427685 0.0955377 0.0132131 0.037602 0.023127 0.141342 0.172065 0.0563155 0.0591369 0.158708 0.0727985 0.0630201 0.0487573 0.608702 2.0 0.196839 0.00318976 0.02054 +0.347553 0.0386982 0.0173799 0.0683621 0.0499532 0.0311773 0.00578328 0.758134 0.0378913 0.310411 0.0802907 0.0153423 0.0288204 0.022131 0.0221486 0.0323591 0.169399 2.0 0.0105123 0.0222037 +0.0196009 0.0276901 0.0148051 0.0181791 0.117574 0.0561089 0.0128298 0.0205964 0.0170585 0.114711 0.0201153 0.00562236 0.0127592 0.0158472 0.10236 0.0728189 0.0135282 0.0518061 2.0 0.17534 +0.0417087 0.0210004 0.0371604 0.0227943 0.4961 0.0172504 0.189266 0.0407279 0.0165324 0.0687289 0.0167114 0.0849022 0.0197739 0.0167267 0.0335535 0.10942 0.0355275 0.0446259 0.0715091 2.0 +numAuxiliaryMatrices(x>0) + 1000 +auxMatrixScaleFactor(x>=1.0) + 2.0 +numProteinTypes(x=0_then_fnaFileName,or,x>0_then_that_many_numOfProteinType_+_set_of_frequencies) + 1 +numOfProteinType[i]_(x>0,_sum_of_numOfProteinType[i=1_to_i=numProteinTypes]_>=minGenomeSize_and_<=maxGenomeSize) + 2500 +freqOf_ACDEFGHIKLMNPQRSTVWY(list_of_20_positive_values_whose_sum_is_1.0) +0.0866279 0.043972 0.0390894 0.0570451 0.0193078 0.0367281 0.0580589 0.0832518 0.0244313 0.048466 0.086209 0.0620286 0.0195027 0.0384319 0.0457631 0.0695179 0.0610127 0.0143859 0.0352742 0.0708956 diff --git a/doc/EvolSimconfigs/evolSimconfig_LGTl25.txt b/doc/EvolSimconfigs/evolSimconfig_LGTl25.txt new file mode 100755 index 0000000000000000000000000000000000000000..3e2cdcabe2f2d10edbc5bcb32a4bbfc57b33db98 --- /dev/null +++ b/doc/EvolSimconfigs/evolSimconfig_LGTl25.txt @@ -0,0 +1,156 @@ +numIterations(x>0) + 5000 +outInterval(x>0,_may_be_>numIterations) + 5001 +rateAndBiasAdjustFrequency(x>0) + 10 +preferredMinNumLineages(x>0) + 25 +maxNumLineages(x>=preferredMinNumLineages) + 35 +speciationAndExtinctionProb(0.0<=x<1.0) + 0.5 +speciationModel{0,1,2} + 1 +selectionModel{0,1,2,3,4} + 0 +numberOfHabitats(x>=1) + 10 +numberOfHabitatNiches(x>=numberOfHabitats) + 100 +numberOfHabitatSpaces(x>=maxNumLineages_&&_x>=numberOfHabitatNiches) + 1000 +probMigrationPerIter(0.0<=x<=1.0) + 0.5 +paralogUsefulnessFactor(x>0.0) + 2.0 +meanNumLGTperIteration(x>=0.0) + 25.0 +exactPropGlobalReq(0.0<=x<=1.0) + 0.02 +meanPropHabReq(0.0<=x<=1.0) + 0.02 +meanPropNicheReq(0.0<=x<=1.0) + 0.01 + +minGenomeSize(x>0) + 2000 +maxGenomeSize(x>=minGenomeSize) + 3000 +initialTargetSize(minGenomeSize<=x<=maxGenomeSize) + 2000 +sizeAdjFactor(x>=0.0) + 1.0 +targetSizeDriftFactor(x>=0.0) + 5.0 + +duplicabilityDriftFactor(0.0<=x<=1.0) + 0.005 +inertiaDriftFactor(0.0<=x<=1.0) + 0.005 +resistanceAdjFactor(0.0<=x<=1.0) + 0.05 +selectiveDriftFactor(0.0<=x<=1.0) + 0.0005 +selectiveDriftBias(0.0<=x<=1.0) + 0.8 +maxInitialSelectivePressure(0.0<x<=1.0) + 0.2 +goodMutationProb(0.0<=x<=1.0) + 0.05 +mutationRateDriftFactor(0.0<=x<=1.0) + 0.005 +minMutationRate(0.0<x<1.0) + 0.1 +maxMutationRate(minMutationRate<=x<1.0) + 0.1 +mutationRate(0.0<x<1.0) + 0.1 +transitionProbDriftFactor(0.0<=x<=1.0) + 0.0005 +minTransitionProb(0.0<x<1.0) + 0.5 +maxTransitionProb(minTransitionProb<=x<1.0) + 0.9 +transitionProb(0.0<x<1.0) + 0.666667 +gcBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minGCbias(0.0<x<1.0) + 0.25 +maxGCbias(minGCbias<=x<1.0) + 0.75 +gcBias(0.0<x<1.0) + 0.5 +purineBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minPurineBias(0.0<x<1.0) + 0.1 +maxPurineBias(minPurineBias<=x<1.0) + 0.25 +purineBias(0.0<x<1.0) + 0.1 + +randomLGTProb(0.0<=x<=1.0) + 1.0 +divergenceLGTProb(0.0<=x<=1.0) + 0.0 +geneCompLGTProb(0.0<=x<=1.0) + 0.0 +gcLGTProb(0.0<=x<=1.0) + 0.0 +habitatLGTProb(0.0<=x<=1.0) + 0.0 + +divergenceFactor(x>0.0,_normally_x<=numIterations) + 5000.0 +geneCompSimilarityFactor(0.0<=x<1.0) + 0.9 +gcSimilarityFactor(0.0<x<=1.0) + 0.9 +orthologReplacementProbability(0.0<=x<=1.0) + 1.0 +lgtReceptivityDriftFactor(0.0<=x<=1.0) + 0.005 +lgtMinReceptivity(0.0<=x<=1.0) + 1.0 +lgtMaxReceptivity(lgtMinReceptivity<=x<=1.0) + 1.0 +lgtReceptivity(0<=x<=1.0) + 1.0 + +minGeneSize(x>0) + 80 +maxGeneSize(x>=minGeneSize) + 500 +substitutionMatrix(list_of_400_positive_values_<=2.0,_ACDEFGHIKLMNPQRSTVWY_x_ACDEFGHIKLMNPQRSTVWY) +2.0 0.0396598 0.0843124 0.183797 0.0161794 0.235889 0.0154872 0.0187403 0.112429 0.0686077 0.0348512 0.0398593 0.131665 0.0667422 0.0485074 0.46866 0.258829 0.284435 0.00325504 0.0169835 +0.177941 2.0 0.00345635 0.00247935 0.0305933 0.0510623 0.0121654 0.0164915 0.00918444 0.066258 0.0152309 0.0207374 0.0100133 0.00725879 0.0464512 0.195715 0.0625971 0.142095 0.0206314 0.0383665 +0.128036 0.00116986 2.0 0.71693 0.00359188 0.144123 0.0454752 0.00382271 0.0595295 0.0146219 0.00404697 0.424466 0.0388056 0.0453065 0.0129545 0.149013 0.0457432 0.0215998 0.00373363 0.0229784 +0.274238 0.00082452 0.704411 2.0 0.00623626 0.0945269 0.0278529 0.0123487 0.320617 0.0265977 0.0122915 0.0740508 0.0624534 0.401766 0.0386212 0.0980118 0.100398 0.0834769 0.00450443 0.0138489 +0.0364693 0.0153698 0.00533148 0.00942109 2.0 0.00831369 0.0331958 0.102697 0.0110207 0.364693 0.046441 0.00751784 0.0147764 0.0073398 0.00903282 0.075904 0.0209765 0.092149 0.0440105 0.455339 +0.245455 0.0118424 0.0987547 0.065922 0.00383789 2.0 0.0121868 0.00295159 0.0463426 0.0105699 0.00679084 0.0879949 0.022293 0.0242444 0.0514178 0.186561 0.0275574 0.02655 0.00969561 0.0073091 +0.0549141 0.0096142 0.106181 0.06619 0.052219 0.0415277 2.0 0.013395 0.110465 0.0861162 0.0157637 0.309298 0.0637204 0.315429 0.18795 0.10291 0.0577555 0.0167821 0.00755458 0.273265 +0.0334964 0.00656987 0.00449938 0.0147928 0.0814349 0.00507005 0.00675232 2.0 0.0401737 0.546732 0.166064 0.0433295 0.0091461 0.00836791 0.0164437 0.0444136 0.177933 1.10899 0.00611352 0.0296423 +0.157016 0.00285886 0.0547468 0.300098 0.00682827 0.0621988 0.0435088 0.0313897 2.0 0.0444071 0.0364418 0.235475 0.0509706 0.286105 0.470625 0.134466 0.169247 0.0433079 0.00395627 0.00940156 +0.0689411 0.0148395 0.00967539 0.0179127 0.16258 0.0102073 0.024405 0.307368 0.0319516 2.0 0.189333 0.0102827 0.0380606 0.0638694 0.0437672 0.0479311 0.0398562 0.255272 0.0191421 0.0281219 +0.154803 0.0150787 0.0118373 0.0365915 0.0915163 0.0289883 0.0197474 0.412684 0.115904 0.83692 2.0 0.0154967 0.0156811 0.113509 0.06008 0.0686705 0.185005 0.29187 0.0148378 0.0302255 +0.0883341 0.010243 0.619444 0.109987 0.00739138 0.18741 0.193315 0.0537232 0.373662 0.0226778 0.00773169 2.0 0.017855 0.11339 0.0558749 0.55256 0.247719 0.027826 0.00206917 0.0766156 +0.249237 0.0042247 0.0483724 0.0792336 0.0124092 0.0405553 0.034018 0.0096863 0.069087 0.071699 0.00668276 0.0152512 2.0 0.068562 0.059757 0.224304 0.0970571 0.0446482 0.00401093 0.0152417 +0.15742 0.00381591 0.0703689 0.635103 0.00768029 0.0549548 0.209821 0.0110422 0.48319 0.149916 0.0602735 0.12068 0.085428 2.0 0.266954 0.14305 0.104689 0.042719 0.00620714 0.0160646 +0.0955629 0.0203964 0.0168059 0.0509939 0.00789476 0.0973488 0.104427 0.0181242 0.663882 0.0858074 0.026647 0.0496706 0.062191 0.222976 2.0 0.170206 0.0676525 0.03571 0.0334881 0.0269165 +0.584009 0.0543576 0.122277 0.081856 0.0419623 0.223418 0.0361666 0.030964 0.119979 0.0594392 0.019265 0.310701 0.147657 0.0755769 0.10766 2.0 0.53423 0.0330003 0.015069 0.0555211 +0.367495 0.0198092 0.0427685 0.0955377 0.0132131 0.037602 0.023127 0.141342 0.172065 0.0563155 0.0591369 0.158708 0.0727985 0.0630201 0.0487573 0.608702 2.0 0.196839 0.00318976 0.02054 +0.347553 0.0386982 0.0173799 0.0683621 0.0499532 0.0311773 0.00578328 0.758134 0.0378913 0.310411 0.0802907 0.0153423 0.0288204 0.022131 0.0221486 0.0323591 0.169399 2.0 0.0105123 0.0222037 +0.0196009 0.0276901 0.0148051 0.0181791 0.117574 0.0561089 0.0128298 0.0205964 0.0170585 0.114711 0.0201153 0.00562236 0.0127592 0.0158472 0.10236 0.0728189 0.0135282 0.0518061 2.0 0.17534 +0.0417087 0.0210004 0.0371604 0.0227943 0.4961 0.0172504 0.189266 0.0407279 0.0165324 0.0687289 0.0167114 0.0849022 0.0197739 0.0167267 0.0335535 0.10942 0.0355275 0.0446259 0.0715091 2.0 +numAuxiliaryMatrices(x>0) + 1000 +auxMatrixScaleFactor(x>=1.0) + 2.0 +numProteinTypes(x=0_then_fnaFileName,or,x>0_then_that_many_numOfProteinType_+_set_of_frequencies) + 1 +numOfProteinType[i]_(x>0,_sum_of_numOfProteinType[i=1_to_i=numProteinTypes]_>=minGenomeSize_and_<=maxGenomeSize) + 2500 +freqOf_ACDEFGHIKLMNPQRSTVWY(list_of_20_positive_values_whose_sum_is_1.0) +0.0866279 0.043972 0.0390894 0.0570451 0.0193078 0.0367281 0.0580589 0.0832518 0.0244313 0.048466 0.086209 0.0620286 0.0195027 0.0384319 0.0457631 0.0695179 0.0610127 0.0143859 0.0352742 0.0708956 diff --git a/doc/EvolSimconfigs/evolSimconfig_LGTl250.txt b/doc/EvolSimconfigs/evolSimconfig_LGTl250.txt new file mode 100755 index 0000000000000000000000000000000000000000..5217dac374ee4fbf30584720338cfc99bc784fad --- /dev/null +++ b/doc/EvolSimconfigs/evolSimconfig_LGTl250.txt @@ -0,0 +1,156 @@ +numIterations(x>0) + 5000 +outInterval(x>0,_may_be_>numIterations) + 5001 +rateAndBiasAdjustFrequency(x>0) + 10 +preferredMinNumLineages(x>0) + 25 +maxNumLineages(x>=preferredMinNumLineages) + 35 +speciationAndExtinctionProb(0.0<=x<1.0) + 0.5 +speciationModel{0,1,2} + 1 +selectionModel{0,1,2,3,4} + 0 +numberOfHabitats(x>=1) + 10 +numberOfHabitatNiches(x>=numberOfHabitats) + 100 +numberOfHabitatSpaces(x>=maxNumLineages_&&_x>=numberOfHabitatNiches) + 1000 +probMigrationPerIter(0.0<=x<=1.0) + 0.5 +paralogUsefulnessFactor(x>0.0) + 2.0 +meanNumLGTperIteration(x>=0.0) + 250.0 +exactPropGlobalReq(0.0<=x<=1.0) + 0.02 +meanPropHabReq(0.0<=x<=1.0) + 0.02 +meanPropNicheReq(0.0<=x<=1.0) + 0.01 + +minGenomeSize(x>0) + 2000 +maxGenomeSize(x>=minGenomeSize) + 3000 +initialTargetSize(minGenomeSize<=x<=maxGenomeSize) + 2000 +sizeAdjFactor(x>=0.0) + 1.0 +targetSizeDriftFactor(x>=0.0) + 5.0 + +duplicabilityDriftFactor(0.0<=x<=1.0) + 0.005 +inertiaDriftFactor(0.0<=x<=1.0) + 0.005 +resistanceAdjFactor(0.0<=x<=1.0) + 0.05 +selectiveDriftFactor(0.0<=x<=1.0) + 0.0005 +selectiveDriftBias(0.0<=x<=1.0) + 0.8 +maxInitialSelectivePressure(0.0<x<=1.0) + 0.2 +goodMutationProb(0.0<=x<=1.0) + 0.05 +mutationRateDriftFactor(0.0<=x<=1.0) + 0.005 +minMutationRate(0.0<x<1.0) + 0.1 +maxMutationRate(minMutationRate<=x<1.0) + 0.1 +mutationRate(0.0<x<1.0) + 0.1 +transitionProbDriftFactor(0.0<=x<=1.0) + 0.0005 +minTransitionProb(0.0<x<1.0) + 0.5 +maxTransitionProb(minTransitionProb<=x<1.0) + 0.9 +transitionProb(0.0<x<1.0) + 0.666667 +gcBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minGCbias(0.0<x<1.0) + 0.25 +maxGCbias(minGCbias<=x<1.0) + 0.75 +gcBias(0.0<x<1.0) + 0.5 +purineBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minPurineBias(0.0<x<1.0) + 0.1 +maxPurineBias(minPurineBias<=x<1.0) + 0.25 +purineBias(0.0<x<1.0) + 0.1 + +randomLGTProb(0.0<=x<=1.0) + 1.0 +divergenceLGTProb(0.0<=x<=1.0) + 0.0 +geneCompLGTProb(0.0<=x<=1.0) + 0.0 +gcLGTProb(0.0<=x<=1.0) + 0.0 +habitatLGTProb(0.0<=x<=1.0) + 0.0 + +divergenceFactor(x>0.0,_normally_x<=numIterations) + 5000.0 +geneCompSimilarityFactor(0.0<=x<1.0) + 0.9 +gcSimilarityFactor(0.0<x<=1.0) + 0.9 +orthologReplacementProbability(0.0<=x<=1.0) + 1.0 +lgtReceptivityDriftFactor(0.0<=x<=1.0) + 0.005 +lgtMinReceptivity(0.0<=x<=1.0) + 1.0 +lgtMaxReceptivity(lgtMinReceptivity<=x<=1.0) + 1.0 +lgtReceptivity(0<=x<=1.0) + 1.0 + +minGeneSize(x>0) + 80 +maxGeneSize(x>=minGeneSize) + 500 +substitutionMatrix(list_of_400_positive_values_<=2.0,_ACDEFGHIKLMNPQRSTVWY_x_ACDEFGHIKLMNPQRSTVWY) +2.0 0.0396598 0.0843124 0.183797 0.0161794 0.235889 0.0154872 0.0187403 0.112429 0.0686077 0.0348512 0.0398593 0.131665 0.0667422 0.0485074 0.46866 0.258829 0.284435 0.00325504 0.0169835 +0.177941 2.0 0.00345635 0.00247935 0.0305933 0.0510623 0.0121654 0.0164915 0.00918444 0.066258 0.0152309 0.0207374 0.0100133 0.00725879 0.0464512 0.195715 0.0625971 0.142095 0.0206314 0.0383665 +0.128036 0.00116986 2.0 0.71693 0.00359188 0.144123 0.0454752 0.00382271 0.0595295 0.0146219 0.00404697 0.424466 0.0388056 0.0453065 0.0129545 0.149013 0.0457432 0.0215998 0.00373363 0.0229784 +0.274238 0.00082452 0.704411 2.0 0.00623626 0.0945269 0.0278529 0.0123487 0.320617 0.0265977 0.0122915 0.0740508 0.0624534 0.401766 0.0386212 0.0980118 0.100398 0.0834769 0.00450443 0.0138489 +0.0364693 0.0153698 0.00533148 0.00942109 2.0 0.00831369 0.0331958 0.102697 0.0110207 0.364693 0.046441 0.00751784 0.0147764 0.0073398 0.00903282 0.075904 0.0209765 0.092149 0.0440105 0.455339 +0.245455 0.0118424 0.0987547 0.065922 0.00383789 2.0 0.0121868 0.00295159 0.0463426 0.0105699 0.00679084 0.0879949 0.022293 0.0242444 0.0514178 0.186561 0.0275574 0.02655 0.00969561 0.0073091 +0.0549141 0.0096142 0.106181 0.06619 0.052219 0.0415277 2.0 0.013395 0.110465 0.0861162 0.0157637 0.309298 0.0637204 0.315429 0.18795 0.10291 0.0577555 0.0167821 0.00755458 0.273265 +0.0334964 0.00656987 0.00449938 0.0147928 0.0814349 0.00507005 0.00675232 2.0 0.0401737 0.546732 0.166064 0.0433295 0.0091461 0.00836791 0.0164437 0.0444136 0.177933 1.10899 0.00611352 0.0296423 +0.157016 0.00285886 0.0547468 0.300098 0.00682827 0.0621988 0.0435088 0.0313897 2.0 0.0444071 0.0364418 0.235475 0.0509706 0.286105 0.470625 0.134466 0.169247 0.0433079 0.00395627 0.00940156 +0.0689411 0.0148395 0.00967539 0.0179127 0.16258 0.0102073 0.024405 0.307368 0.0319516 2.0 0.189333 0.0102827 0.0380606 0.0638694 0.0437672 0.0479311 0.0398562 0.255272 0.0191421 0.0281219 +0.154803 0.0150787 0.0118373 0.0365915 0.0915163 0.0289883 0.0197474 0.412684 0.115904 0.83692 2.0 0.0154967 0.0156811 0.113509 0.06008 0.0686705 0.185005 0.29187 0.0148378 0.0302255 +0.0883341 0.010243 0.619444 0.109987 0.00739138 0.18741 0.193315 0.0537232 0.373662 0.0226778 0.00773169 2.0 0.017855 0.11339 0.0558749 0.55256 0.247719 0.027826 0.00206917 0.0766156 +0.249237 0.0042247 0.0483724 0.0792336 0.0124092 0.0405553 0.034018 0.0096863 0.069087 0.071699 0.00668276 0.0152512 2.0 0.068562 0.059757 0.224304 0.0970571 0.0446482 0.00401093 0.0152417 +0.15742 0.00381591 0.0703689 0.635103 0.00768029 0.0549548 0.209821 0.0110422 0.48319 0.149916 0.0602735 0.12068 0.085428 2.0 0.266954 0.14305 0.104689 0.042719 0.00620714 0.0160646 +0.0955629 0.0203964 0.0168059 0.0509939 0.00789476 0.0973488 0.104427 0.0181242 0.663882 0.0858074 0.026647 0.0496706 0.062191 0.222976 2.0 0.170206 0.0676525 0.03571 0.0334881 0.0269165 +0.584009 0.0543576 0.122277 0.081856 0.0419623 0.223418 0.0361666 0.030964 0.119979 0.0594392 0.019265 0.310701 0.147657 0.0755769 0.10766 2.0 0.53423 0.0330003 0.015069 0.0555211 +0.367495 0.0198092 0.0427685 0.0955377 0.0132131 0.037602 0.023127 0.141342 0.172065 0.0563155 0.0591369 0.158708 0.0727985 0.0630201 0.0487573 0.608702 2.0 0.196839 0.00318976 0.02054 +0.347553 0.0386982 0.0173799 0.0683621 0.0499532 0.0311773 0.00578328 0.758134 0.0378913 0.310411 0.0802907 0.0153423 0.0288204 0.022131 0.0221486 0.0323591 0.169399 2.0 0.0105123 0.0222037 +0.0196009 0.0276901 0.0148051 0.0181791 0.117574 0.0561089 0.0128298 0.0205964 0.0170585 0.114711 0.0201153 0.00562236 0.0127592 0.0158472 0.10236 0.0728189 0.0135282 0.0518061 2.0 0.17534 +0.0417087 0.0210004 0.0371604 0.0227943 0.4961 0.0172504 0.189266 0.0407279 0.0165324 0.0687289 0.0167114 0.0849022 0.0197739 0.0167267 0.0335535 0.10942 0.0355275 0.0446259 0.0715091 2.0 +numAuxiliaryMatrices(x>0) + 1000 +auxMatrixScaleFactor(x>=1.0) + 2.0 +numProteinTypes(x=0_then_fnaFileName,or,x>0_then_that_many_numOfProteinType_+_set_of_frequencies) + 1 +numOfProteinType[i]_(x>0,_sum_of_numOfProteinType[i=1_to_i=numProteinTypes]_>=minGenomeSize_and_<=maxGenomeSize) + 2500 +freqOf_ACDEFGHIKLMNPQRSTVWY(list_of_20_positive_values_whose_sum_is_1.0) +0.0866279 0.043972 0.0390894 0.0570451 0.0193078 0.0367281 0.0580589 0.0832518 0.0244313 0.048466 0.086209 0.0620286 0.0195027 0.0384319 0.0457631 0.0695179 0.0610127 0.0143859 0.0352742 0.0708956 diff --git a/doc/EvolSimconfigs/evolSimconfig_LGTl5.txt b/doc/EvolSimconfigs/evolSimconfig_LGTl5.txt new file mode 100755 index 0000000000000000000000000000000000000000..085f3cf5a9b35df4ddfd5d10da25de0db03ffa5e --- /dev/null +++ b/doc/EvolSimconfigs/evolSimconfig_LGTl5.txt @@ -0,0 +1,156 @@ +numIterations(x>0) + 5000 +outInterval(x>0,_may_be_>numIterations) + 5001 +rateAndBiasAdjustFrequency(x>0) + 10 +preferredMinNumLineages(x>0) + 25 +maxNumLineages(x>=preferredMinNumLineages) + 35 +speciationAndExtinctionProb(0.0<=x<1.0) + 0.5 +speciationModel{0,1,2} + 1 +selectionModel{0,1,2,3,4} + 0 +numberOfHabitats(x>=1) + 10 +numberOfHabitatNiches(x>=numberOfHabitats) + 100 +numberOfHabitatSpaces(x>=maxNumLineages_&&_x>=numberOfHabitatNiches) + 1000 +probMigrationPerIter(0.0<=x<=1.0) + 0.5 +paralogUsefulnessFactor(x>0.0) + 2.0 +meanNumLGTperIteration(x>=0.0) + 5.0 +exactPropGlobalReq(0.0<=x<=1.0) + 0.02 +meanPropHabReq(0.0<=x<=1.0) + 0.02 +meanPropNicheReq(0.0<=x<=1.0) + 0.01 + +minGenomeSize(x>0) + 2000 +maxGenomeSize(x>=minGenomeSize) + 3000 +initialTargetSize(minGenomeSize<=x<=maxGenomeSize) + 2000 +sizeAdjFactor(x>=0.0) + 1.0 +targetSizeDriftFactor(x>=0.0) + 5.0 + +duplicabilityDriftFactor(0.0<=x<=1.0) + 0.005 +inertiaDriftFactor(0.0<=x<=1.0) + 0.005 +resistanceAdjFactor(0.0<=x<=1.0) + 0.05 +selectiveDriftFactor(0.0<=x<=1.0) + 0.0005 +selectiveDriftBias(0.0<=x<=1.0) + 0.8 +maxInitialSelectivePressure(0.0<x<=1.0) + 0.2 +goodMutationProb(0.0<=x<=1.0) + 0.05 +mutationRateDriftFactor(0.0<=x<=1.0) + 0.005 +minMutationRate(0.0<x<1.0) + 0.1 +maxMutationRate(minMutationRate<=x<1.0) + 0.1 +mutationRate(0.0<x<1.0) + 0.1 +transitionProbDriftFactor(0.0<=x<=1.0) + 0.0005 +minTransitionProb(0.0<x<1.0) + 0.5 +maxTransitionProb(minTransitionProb<=x<1.0) + 0.9 +transitionProb(0.0<x<1.0) + 0.666667 +gcBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minGCbias(0.0<x<1.0) + 0.25 +maxGCbias(minGCbias<=x<1.0) + 0.75 +gcBias(0.0<x<1.0) + 0.5 +purineBiasDriftFactor(0.0<=x<=1.0) + 0.005 +minPurineBias(0.0<x<1.0) + 0.1 +maxPurineBias(minPurineBias<=x<1.0) + 0.25 +purineBias(0.0<x<1.0) + 0.1 + +randomLGTProb(0.0<=x<=1.0) + 1.0 +divergenceLGTProb(0.0<=x<=1.0) + 0.0 +geneCompLGTProb(0.0<=x<=1.0) + 0.0 +gcLGTProb(0.0<=x<=1.0) + 0.0 +habitatLGTProb(0.0<=x<=1.0) + 0.0 + +divergenceFactor(x>0.0,_normally_x<=numIterations) + 5000.0 +geneCompSimilarityFactor(0.0<=x<1.0) + 0.9 +gcSimilarityFactor(0.0<x<=1.0) + 0.9 +orthologReplacementProbability(0.0<=x<=1.0) + 1.0 +lgtReceptivityDriftFactor(0.0<=x<=1.0) + 0.005 +lgtMinReceptivity(0.0<=x<=1.0) + 1.0 +lgtMaxReceptivity(lgtMinReceptivity<=x<=1.0) + 1.0 +lgtReceptivity(0<=x<=1.0) + 1.0 + +minGeneSize(x>0) + 80 +maxGeneSize(x>=minGeneSize) + 500 +substitutionMatrix(list_of_400_positive_values_<=2.0,_ACDEFGHIKLMNPQRSTVWY_x_ACDEFGHIKLMNPQRSTVWY) +2.0 0.0396598 0.0843124 0.183797 0.0161794 0.235889 0.0154872 0.0187403 0.112429 0.0686077 0.0348512 0.0398593 0.131665 0.0667422 0.0485074 0.46866 0.258829 0.284435 0.00325504 0.0169835 +0.177941 2.0 0.00345635 0.00247935 0.0305933 0.0510623 0.0121654 0.0164915 0.00918444 0.066258 0.0152309 0.0207374 0.0100133 0.00725879 0.0464512 0.195715 0.0625971 0.142095 0.0206314 0.0383665 +0.128036 0.00116986 2.0 0.71693 0.00359188 0.144123 0.0454752 0.00382271 0.0595295 0.0146219 0.00404697 0.424466 0.0388056 0.0453065 0.0129545 0.149013 0.0457432 0.0215998 0.00373363 0.0229784 +0.274238 0.00082452 0.704411 2.0 0.00623626 0.0945269 0.0278529 0.0123487 0.320617 0.0265977 0.0122915 0.0740508 0.0624534 0.401766 0.0386212 0.0980118 0.100398 0.0834769 0.00450443 0.0138489 +0.0364693 0.0153698 0.00533148 0.00942109 2.0 0.00831369 0.0331958 0.102697 0.0110207 0.364693 0.046441 0.00751784 0.0147764 0.0073398 0.00903282 0.075904 0.0209765 0.092149 0.0440105 0.455339 +0.245455 0.0118424 0.0987547 0.065922 0.00383789 2.0 0.0121868 0.00295159 0.0463426 0.0105699 0.00679084 0.0879949 0.022293 0.0242444 0.0514178 0.186561 0.0275574 0.02655 0.00969561 0.0073091 +0.0549141 0.0096142 0.106181 0.06619 0.052219 0.0415277 2.0 0.013395 0.110465 0.0861162 0.0157637 0.309298 0.0637204 0.315429 0.18795 0.10291 0.0577555 0.0167821 0.00755458 0.273265 +0.0334964 0.00656987 0.00449938 0.0147928 0.0814349 0.00507005 0.00675232 2.0 0.0401737 0.546732 0.166064 0.0433295 0.0091461 0.00836791 0.0164437 0.0444136 0.177933 1.10899 0.00611352 0.0296423 +0.157016 0.00285886 0.0547468 0.300098 0.00682827 0.0621988 0.0435088 0.0313897 2.0 0.0444071 0.0364418 0.235475 0.0509706 0.286105 0.470625 0.134466 0.169247 0.0433079 0.00395627 0.00940156 +0.0689411 0.0148395 0.00967539 0.0179127 0.16258 0.0102073 0.024405 0.307368 0.0319516 2.0 0.189333 0.0102827 0.0380606 0.0638694 0.0437672 0.0479311 0.0398562 0.255272 0.0191421 0.0281219 +0.154803 0.0150787 0.0118373 0.0365915 0.0915163 0.0289883 0.0197474 0.412684 0.115904 0.83692 2.0 0.0154967 0.0156811 0.113509 0.06008 0.0686705 0.185005 0.29187 0.0148378 0.0302255 +0.0883341 0.010243 0.619444 0.109987 0.00739138 0.18741 0.193315 0.0537232 0.373662 0.0226778 0.00773169 2.0 0.017855 0.11339 0.0558749 0.55256 0.247719 0.027826 0.00206917 0.0766156 +0.249237 0.0042247 0.0483724 0.0792336 0.0124092 0.0405553 0.034018 0.0096863 0.069087 0.071699 0.00668276 0.0152512 2.0 0.068562 0.059757 0.224304 0.0970571 0.0446482 0.00401093 0.0152417 +0.15742 0.00381591 0.0703689 0.635103 0.00768029 0.0549548 0.209821 0.0110422 0.48319 0.149916 0.0602735 0.12068 0.085428 2.0 0.266954 0.14305 0.104689 0.042719 0.00620714 0.0160646 +0.0955629 0.0203964 0.0168059 0.0509939 0.00789476 0.0973488 0.104427 0.0181242 0.663882 0.0858074 0.026647 0.0496706 0.062191 0.222976 2.0 0.170206 0.0676525 0.03571 0.0334881 0.0269165 +0.584009 0.0543576 0.122277 0.081856 0.0419623 0.223418 0.0361666 0.030964 0.119979 0.0594392 0.019265 0.310701 0.147657 0.0755769 0.10766 2.0 0.53423 0.0330003 0.015069 0.0555211 +0.367495 0.0198092 0.0427685 0.0955377 0.0132131 0.037602 0.023127 0.141342 0.172065 0.0563155 0.0591369 0.158708 0.0727985 0.0630201 0.0487573 0.608702 2.0 0.196839 0.00318976 0.02054 +0.347553 0.0386982 0.0173799 0.0683621 0.0499532 0.0311773 0.00578328 0.758134 0.0378913 0.310411 0.0802907 0.0153423 0.0288204 0.022131 0.0221486 0.0323591 0.169399 2.0 0.0105123 0.0222037 +0.0196009 0.0276901 0.0148051 0.0181791 0.117574 0.0561089 0.0128298 0.0205964 0.0170585 0.114711 0.0201153 0.00562236 0.0127592 0.0158472 0.10236 0.0728189 0.0135282 0.0518061 2.0 0.17534 +0.0417087 0.0210004 0.0371604 0.0227943 0.4961 0.0172504 0.189266 0.0407279 0.0165324 0.0687289 0.0167114 0.0849022 0.0197739 0.0167267 0.0335535 0.10942 0.0355275 0.0446259 0.0715091 2.0 +numAuxiliaryMatrices(x>0) + 1000 +auxMatrixScaleFactor(x>=1.0) + 2.0 +numProteinTypes(x=0_then_fnaFileName,or,x>0_then_that_many_numOfProteinType_+_set_of_frequencies) + 1 +numOfProteinType[i]_(x>0,_sum_of_numOfProteinType[i=1_to_i=numProteinTypes]_>=minGenomeSize_and_<=maxGenomeSize) + 2500 +freqOf_ACDEFGHIKLMNPQRSTVWY(list_of_20_positive_values_whose_sum_is_1.0) +0.0866279 0.043972 0.0390894 0.0570451 0.0193078 0.0367281 0.0580589 0.0832518 0.0244313 0.048466 0.086209 0.0620286 0.0195027 0.0384319 0.0457631 0.0695179 0.0610127 0.0143859 0.0352742 0.0708956