--- GDE/MrBAYES/mrbayes_3.2.1/model.c.orig	2016-05-02 19:19:07.000000000 +0800
+++ GDE/MrBAYES/mrbayes_3.2.1/model.c	2026-05-22 05:50:37.000000000 +0800
@@ -155,9 +155,9 @@
 
 
 /* parser flags and variables */
-int         fromI, toJ, foundDash, foundComma, foundEqual, foundBeta,
-            foundAaSetting, foundExp, modelIsFixed, linkNum, foundLeftPar,
-            tempNumStates, isNegative;
+int         modelFromI, modelToJ, modelFoundDash, foundComma, modelFoundEqual, foundBeta,
+            foundAaSetting, modelFoundExp, modelIsFixed, linkNum, foundLeftPar,
+            tempNumStates, modelIsNegative;
 MrBFlt      tempStateFreqs[200], tempAaModelPrs[10];
 char		colonPr[100], clockPr[30];
 
@@ -1094,7 +1094,7 @@
 int ChangeNumChains (int from, int to)
 
 {
-	int			i, i1, j, k, m, st, nRuns, fromIndex, toIndex, run, chn, *tempIntVals, nCppEventParams, *toEvents, *fromEvents;
+	int			i, i1, j, k, m, st, nRuns, modelFromIndex, toIndex, run, chn, *tempIntVals, nCppEventParams, *toEvents, *fromEvents;
 	MCMCMove	**tempMoves, *fromMove, *toMove;
 	Tree		**tempTrees;
 	MrBFlt		*tempVals, **toRateMult, **toPosition, **fromRateMult, **fromPosition, *stdStateFreqsOld;
@@ -1157,26 +1157,26 @@
 			{
 			if (chn < to)
 				{
-				fromIndex = (run*from + chn)*2*paramValsRowSize;
+				modelFromIndex = (run*from + chn)*2*paramValsRowSize;
 				toIndex = (run*to + chn)*2*paramValsRowSize;
 				for (i=0; i<2*paramValsRowSize; i++)
-					paramValues[toIndex++] = tempVals[fromIndex++];
-				fromIndex = (run*from + chn)*2*intValsRowSize;
+					paramValues[toIndex++] = tempVals[modelFromIndex++];
+				modelFromIndex = (run*from + chn)*2*intValsRowSize;
 				toIndex = (run*to + chn)*2*intValsRowSize;
 				for (i=0; i<2*intValsRowSize; i++)
-					intValues[toIndex++] = tempIntVals[fromIndex++];
+					intValues[toIndex++] = tempIntVals[modelFromIndex++];
                 for (i=i1=0; i<numParams; i++)
                     {
                     p = &params[i];
                     if (p->paramType == P_CPPEVENTS)
                         {
-                        fromIndex = 2*(run*from + chn);
+                        modelFromIndex = 2*(run*from + chn);
                         toIndex = 2*(run*to + chn);
-                        fromEvents = cppEventParams[i1].nEvents[fromIndex];
+                        fromEvents = cppEventParams[i1].nEvents[modelFromIndex];
                         toEvents = p->nEvents[toIndex];
-                        fromPosition = cppEventParams[i1].position[fromIndex];
+                        fromPosition = cppEventParams[i1].position[modelFromIndex];
                         toPosition = p->position[toIndex];
-                        fromRateMult = cppEventParams[i1].rateMult[fromIndex];
+                        fromRateMult = cppEventParams[i1].rateMult[modelFromIndex];
                         toRateMult = p->rateMult[toIndex];
                         for (j=0; j<2*numLocalTaxa; j++)
                             {
@@ -1230,12 +1230,12 @@
             if (chn >= to)
                 continue;
             /*Here we move only one tree per chain/state?! Should not we move numTrees??*/
-            fromIndex = 2*(run*from + chn)  * numTrees;
+            modelFromIndex = 2*(run*from + chn)  * numTrees;
             toIndex   = 2*(run*to   + chn)  * numTrees;
             for(k=0;k<2*numTrees;k++)
                 {
-                mcmcTree[toIndex+k]    = tempTrees[fromIndex+k];
-                tempTrees[fromIndex+k] = NULL;
+                mcmcTree[toIndex+k]    = tempTrees[modelFromIndex+k];
+                tempTrees[modelFromIndex+k] = NULL;
                 }
             }
         }
@@ -1328,11 +1328,11 @@
                 if (chn >= to)
                     break;
 
-                fromIndex = 2*(run*from + chn)*stdStateFreqsRowSize;
+                modelFromIndex = 2*(run*from + chn)*stdStateFreqsRowSize;
                 toIndex = 2*(run*to + chn)*stdStateFreqsRowSize;
                 for(k=0;k<2*stdStateFreqsRowSize;k++)
                     {
-                    stdStateFreqs[toIndex+k]=stdStateFreqsOld[fromIndex+k];
+                    stdStateFreqs[toIndex+k]=stdStateFreqsOld[modelFromIndex+k];
                     }
                 }
             /* set new chains */
@@ -1360,12 +1360,12 @@
 				{
 				if (chn < to)
 					{
-					fromIndex = run*from + chn;
+					modelFromIndex = run*from + chn;
 					toIndex = run*to + chn;
-					toMove->relProposalProb[toIndex] = fromMove->relProposalProb[fromIndex];
+					toMove->relProposalProb[toIndex] = fromMove->relProposalProb[modelFromIndex];
 					for (j=0; j<toMove->moveType->numTuningParams; j++)
 						{
-						toMove->tuningParam[toIndex][j] = fromMove->tuningParam[fromIndex][j];
+						toMove->tuningParam[toIndex][j] = fromMove->tuningParam[modelFromIndex][j];
 						}
 					}
 				}
@@ -2849,14 +2849,14 @@
 		/* initialize tempLinkUnlinkVec to no */
 		for (i=0; i<numCurrentDivisions; i++)
 			tempLinkUnlinkVec[i] = NO;
-		fromI = toJ = -1;
-		foundDash = NO;
+		modelFromI = modelToJ = -1;
+		modelFoundDash = NO;
 		expecting = Expecting(NUMBER) | Expecting(ALPHA);
 		}
 	else if (expecting == Expecting(RIGHTPAR))
 		{
-		if (fromI != -1)
-			tempLinkUnlinkVec[fromI-1] = YES;
+		if (modelFromI != -1)
+			tempLinkUnlinkVec[modelFromI-1] = YES;
 		/* now copy tempLinkUnlinkVec to appropriate row of tempLinkUnlink */
 		if (!strcmp(parmName, "Tratio"))
 			{
@@ -3004,20 +3004,20 @@
 			MrBayesPrint ("%s   Partition delimiter is too large\n", spacer);
 			return (ERROR);
 			}
-		if (fromI == -1)
-			fromI = tempInt;
-		else if (fromI != -1 && toJ == -1 && foundDash == YES && foundComma == NO)
+		if (modelFromI == -1)
+			modelFromI = tempInt;
+		else if (modelFromI != -1 && modelToJ == -1 && modelFoundDash == YES && foundComma == NO)
 			{
-			toJ = tempInt;
-			for (i=fromI-1; i<toJ; i++)
+			modelToJ = tempInt;
+			for (i=modelFromI-1; i<modelToJ; i++)
 				tempLinkUnlinkVec[i] = YES;
-			fromI = toJ = -1;
-			foundDash = NO;
+			modelFromI = modelToJ = -1;
+			modelFoundDash = NO;
 			}
-		else if (fromI != -1 && toJ == -1 && foundDash == NO && foundComma == YES)
+		else if (modelFromI != -1 && modelToJ == -1 && modelFoundDash == NO && foundComma == YES)
 			{
-			tempLinkUnlinkVec[fromI-1] = YES;
-			fromI = tempInt;
+			tempLinkUnlinkVec[modelFromI-1] = YES;
+			modelFromI = tempInt;
 			foundComma = NO;
 			}
 		expecting  = Expecting(COMMA);
@@ -3026,7 +3026,7 @@
 		}
 	else if (expecting == Expecting(DASH))
 		{
-		foundDash = YES;
+		modelFoundDash = YES;
 		expecting = Expecting(NUMBER);
 		}
 	else
@@ -3134,14 +3134,14 @@
 				{
 				for (i=0; i<numCurrentDivisions; i++)
 					activeParts[i] = NO;
-				fromI = toJ = -1;
-				foundDash = NO;
+				modelFromI = modelToJ = -1;
+				modelFoundDash = NO;
 				expecting = Expecting(NUMBER) | Expecting(ALPHA);
 				}
 			else if (expecting == Expecting(RIGHTPAR))
 				{
-				if (fromI != -1)
-					activeParts[fromI-1] = YES;
+				if (modelFromI != -1)
+					activeParts[modelFromI-1] = YES;
 				expecting = Expecting(PARAMETER) | Expecting(SEMICOLON);
 				}
 			else if (expecting == Expecting(COMMA))
@@ -3168,20 +3168,20 @@
 					MrBayesPrint ("%s   Partition delimiter is too large\n", spacer);
 					return (ERROR);
 					}
-				if (fromI == -1)
-					fromI = tempInt;
-				else if (fromI != -1 && toJ == -1 && foundDash == YES && foundComma == NO)
+				if (modelFromI == -1)
+					modelFromI = tempInt;
+				else if (modelFromI != -1 && modelToJ == -1 && modelFoundDash == YES && foundComma == NO)
 					{
-					toJ = tempInt;
-					for (i=fromI-1; i<toJ; i++)
+					modelToJ = tempInt;
+					for (i=modelFromI-1; i<modelToJ; i++)
 						activeParts[i] = YES;
-					fromI = toJ = -1;
-					foundDash = NO;
+					modelFromI = modelToJ = -1;
+					modelFoundDash = NO;
 					}
-				else if (fromI != -1 && toJ == -1 && foundDash == NO && foundComma == YES)
+				else if (modelFromI != -1 && modelToJ == -1 && modelFoundDash == NO && foundComma == YES)
 					{
-					activeParts[fromI-1] = YES;
-					fromI = tempInt;
+					activeParts[modelFromI-1] = YES;
+					modelFromI = tempInt;
 					foundComma = NO;
 					}
 					
@@ -3191,7 +3191,7 @@
 				}
 			else if (expecting == Expecting(DASH))
 				{
-				foundDash = YES;
+				modelFoundDash = YES;
 				expecting = Expecting(NUMBER);
 				}
 			else
@@ -3835,7 +3835,7 @@
 			/* copy to local move name */
             SafeStrcpy(&tempName, tkn);
 			mv = NULL;
-			foundComma = foundEqual = NO;
+			foundComma = modelFoundEqual = NO;
 			expecting = Expecting(LEFTCURL) | Expecting(RIGHTCURL) | Expecting(COMMA) |
 				Expecting(LEFTPAR) | Expecting(RIGHTPAR) | Expecting(NUMBER) | Expecting(ALPHA) |
 				Expecting(DOLLAR);
@@ -3962,7 +3962,7 @@
 		else
 			mv = moves[j];
 
-		foundComma = foundEqual = NO;
+		foundComma = modelFoundEqual = NO;
 		expecting = Expecting(ALPHA);
 		}
 	else if (expecting == Expecting(LEFTPAR))
@@ -3991,7 +3991,7 @@
 				Expecting(LEFTPAR) | Expecting(RIGHTPAR) | Expecting(NUMBER) | Expecting(ALPHA) |
 				Expecting(DOLLAR);
 			}
-		else if (foundEqual == YES)
+		else if (modelFoundEqual == YES)
 			{
 			sscanf (tkn, "%lf", &tempFloat);
 			if (tempFloat < theValueMin || tempFloat > theValueMax)
@@ -4034,7 +4034,7 @@
 				}
 			expecting = Expecting (PARAMETER) | Expecting(SEMICOLON);
 			}
-		else /* if (foundEqual == NO) */
+		else /* if (modelFoundEqual == NO) */
 			{
 			sscanf (tkn, "%d", &tempInt);
 			if (foundComma == NO)
@@ -4091,7 +4091,7 @@
 		}
 	else if (expecting == Expecting(EQUALSIGN))
 		{
-		foundEqual = YES;
+		modelFoundEqual = YES;
 		expecting = Expecting(NUMBER);
 		}
 	else
@@ -4201,14 +4201,14 @@
 				{
 				for (i=0; i<numCurrentDivisions; i++)
 					activeParts[i] = NO;
-				fromI = toJ = -1;
-				foundDash = NO;
+				modelFromI = modelToJ = -1;
+				modelFoundDash = NO;
 				expecting = Expecting(NUMBER) | Expecting(ALPHA);
 				}
 			else if (expecting == Expecting(RIGHTPAR))
 				{
-				if (fromI != -1)
-					activeParts[fromI-1] = YES;
+				if (modelFromI != -1)
+					activeParts[modelFromI-1] = YES;
 #				if 0
 				for (i=0; i<numCurrentDivisions; i++)
 					MrBayesPrint("%d ", activeParts[i]);
@@ -4240,20 +4240,20 @@
 					MrBayesPrint ("%s   Partition delimiter is too large\n", spacer);
 					return (ERROR);
 					}
-				if (fromI == -1)
-					fromI = tempInt;
-				else if (fromI != -1 && toJ == -1 && foundDash == YES && foundComma == NO)
+				if (modelFromI == -1)
+					modelFromI = tempInt;
+				else if (modelFromI != -1 && modelToJ == -1 && modelFoundDash == YES && foundComma == NO)
 					{
-					toJ = tempInt;
-					for (i=fromI-1; i<toJ; i++)
+					modelToJ = tempInt;
+					for (i=modelFromI-1; i<modelToJ; i++)
 						activeParts[i] = YES;
-					fromI = toJ = -1;
-					foundDash = NO;
+					modelFromI = modelToJ = -1;
+					modelFoundDash = NO;
 					}
-				else if (fromI != -1 && toJ == -1 && foundDash == NO && foundComma == YES)
+				else if (modelFromI != -1 && modelToJ == -1 && modelFoundDash == NO && foundComma == YES)
 					{
-					activeParts[fromI-1] = YES;
-					fromI = tempInt;
+					activeParts[modelFromI-1] = YES;
+					modelFromI = tempInt;
 					foundComma = NO;
 					}
 					
@@ -4263,7 +4263,7 @@
 				}
 			else if (expecting == Expecting(DASH))
 				{
-				foundDash = YES;
+				modelFoundDash = YES;
 				expecting = Expecting(NUMBER);
 				}
 			else
@@ -5516,7 +5516,7 @@
 				expecting  = Expecting(LEFTPAR);
 				for (i=0; i<numCurrentDivisions; i++)
 					numVars[i] = 0;
-				foundDash = NO;
+				modelFoundDash = NO;
 				}
 			else if (expecting == Expecting(LEFTPAR))
 				{
@@ -5532,7 +5532,7 @@
 						if (!strcmp(modelParams[i].adGammaCorPr,"Uniform"))
 							{
 							sscanf (tkn, "%lf", &tempD);
-							if (foundDash == YES)
+							if (modelFoundDash == YES)
 							tempD *= -1.0;
 							modelParams[i].corrUni[numVars[i]++] = tempD;
 							if (numVars[i] == 1)
@@ -5564,7 +5564,7 @@
 						else if (!strcmp(modelParams[i].adGammaCorPr,"Fixed"))
 							{
 							sscanf (tkn, "%lf", &tempD);
-							if (foundDash == YES)
+							if (modelFoundDash == YES)
 								tempD *= -1.0;
 							if (tempD > 1.0 || tempD < -1.0)
 								{
@@ -5580,11 +5580,11 @@
 							}
 						}
 					}
-				foundDash = NO;
+				modelFoundDash = NO;
 				}
 			else if (expecting == Expecting(DASH))
 				{
-				foundDash = YES;
+				modelFoundDash = YES;
 				expecting  = Expecting(NUMBER);
 				}
 			else if (expecting == Expecting(COMMA))
@@ -5631,7 +5631,7 @@
 				expecting  = Expecting(LEFTPAR);
 				for (i=0; i<numCurrentDivisions; i++)
 					numVars[i] = 0;
-				foundDash = NO;
+				modelFoundDash = NO;
 				}
 			else if (expecting == Expecting(LEFTPAR))
 				{
@@ -5647,7 +5647,7 @@
 						if (!strcmp(modelParams[i].brownCorPr,"Uniform"))
 							{
 							sscanf (tkn, "%lf", &tempD);
-							if (foundDash == YES)
+							if (modelFoundDash == YES)
 							tempD *= -1.0;
 							modelParams[i].brownCorrUni[numVars[i]++] = tempD;
 							if (numVars[i] == 1)
@@ -5679,7 +5679,7 @@
 						else if (!strcmp(modelParams[i].brownCorPr,"Fixed"))
 							{
 							sscanf (tkn, "%lf", &tempD);
-							if (foundDash == YES)
+							if (modelFoundDash == YES)
 								tempD *= -1.0;
 							if (tempD > 1.0 || tempD < -1.0)
 								{
@@ -5695,11 +5695,11 @@
 							}
 						}
 					}
-				foundDash = NO;
+				modelFoundDash = NO;
 				}
 			else if (expecting == Expecting(DASH))
 				{
-				foundDash = YES;
+				modelFoundDash = YES;
 				expecting  = Expecting(NUMBER);
 				}
 			else if (expecting == Expecting(COMMA))
@@ -6299,12 +6299,12 @@
 			{
 			if (expecting == Expecting(EQUALSIGN))
 				{
-				foundEqual = YES;
+				modelFoundEqual = YES;
 				expecting = Expecting(ALPHA);
 				}
 			else if (expecting == Expecting(ALPHA))
 				{
-				if (foundEqual == YES)
+				if (modelFoundEqual == YES)
 					{
 					if (IsArgValid(tkn, tempStr) == NO_ERROR)
 						{
@@ -6335,7 +6335,7 @@
 						expecting = Expecting(PARAMETER) | Expecting(SEMICOLON);
 					else
 						expecting = Expecting(LEFTPAR);
-					foundEqual = NO;
+					modelFoundEqual = NO;
 					}
 				else
 					{
@@ -6345,7 +6345,7 @@
 					    if (activeParts[i] == YES || nApplied == 0)
                             break;
 
-					if (foundDash == YES)   /* we must be collecting constraint numbers */
+					if (modelFoundDash == YES)   /* we must be collecting constraint numbers */
 						{
                         MrBayesPrint ("%s   Expecting a number\n", spacer);
 						return (ERROR);
@@ -6370,7 +6370,7 @@
 						    MrBayesPrint ("%s   Could not set fixed topology from user tree '%s'\n", spacer, tkn);
 						    return (ERROR);
   						    }
-                        fromI = index + 1;        /* fromI is used to hold the index of the user tree, 1-based */
+                        modelFromI = index + 1;        /* modelFromI is used to hold the index of the user tree, 1-based */
                         expecting = Expecting(RIGHTPAR);
                         }
 					}
@@ -6379,8 +6379,8 @@
 				{
 				for (i=0; i<numDefinedConstraints; i++)
 					tempActiveConstraints[i] = NO;
-				fromI = toJ = -1;
-				foundDash = foundComma = NO;
+				modelFromI = modelToJ = -1;
+				modelFoundDash = foundComma = NO;
 				expecting = Expecting(NUMBER) | Expecting(ALPHA);
 				}
 			else if (expecting == Expecting(NUMBER))
@@ -6404,29 +6404,29 @@
 					    MrBayesPrint ("%s   Constraint number is too large\n", spacer);
 					    return (ERROR);
 					    }
-                    if (fromI == -1)
+                    if (modelFromI == -1)
                         {
-				        if ( foundDash == YES )
+				        if ( modelFoundDash == YES )
 					        {
 					        MrBayesPrint ("%s   Unexpected dash\n", spacer);
 					        return (ERROR);
 					        }
-                        fromI = tempInt;
-                        tempActiveConstraints[fromI-1] = YES;
+                        modelFromI = tempInt;
+                        tempActiveConstraints[modelFromI-1] = YES;
                         }
-				    else if (fromI != -1 && toJ == -1 && foundDash == YES && foundComma == NO)
+				    else if (modelFromI != -1 && modelToJ == -1 && modelFoundDash == YES && foundComma == NO)
 					    {
-					    toJ = tempInt;
-					    //for (i=fromI-1; i<toJ; i++)
-                        for (i=fromI; i<toJ; i++)
+					    modelToJ = tempInt;
+					    //for (i=modelFromI-1; i<modelToJ; i++)
+                        for (i=modelFromI; i<modelToJ; i++)
 						    tempActiveConstraints[i] = YES;
-					    fromI = toJ = -1;
-					    foundDash = NO;
+					    modelFromI = modelToJ = -1;
+					    modelFoundDash = NO;
 					    }
-				    else if (fromI != -1 && toJ == -1 && foundDash == NO && foundComma == YES)
+				    else if (modelFromI != -1 && modelToJ == -1 && modelFoundDash == NO && foundComma == YES)
 					    {
-					    fromI = tempInt;
-                        tempActiveConstraints[fromI-1] = YES;
+					    modelFromI = tempInt;
+                        tempActiveConstraints[modelFromI-1] = YES;
 					    foundComma = NO;
 					    }
 				    expecting  = Expecting(COMMA);
@@ -6451,7 +6451,7 @@
 					    MrBayesPrint ("%s   Tree number is too small\n", spacer);
 					    return (ERROR);
 					    }
-				    fromI = tempInt;
+				    modelFromI = tempInt;
 				    expecting = Expecting(RIGHTPAR);    /* only one tree number acceptable */
                     }
                 }
@@ -6462,7 +6462,7 @@
 				}
 			else if (expecting == Expecting(DASH))
 				{
-				foundDash = YES;
+				modelFoundDash = YES;
 				expecting = Expecting(NUMBER);
 				}
 			else if (expecting == Expecting(RIGHTPAR))
@@ -6505,7 +6505,7 @@
 			        for (i=0; i<numCurrentDivisions; i++)
 				        {
 				        if (activeParts[i] == YES || nApplied == 0)
-					        modelParams[i].topologyFix = fromI-1;
+					        modelParams[i].topologyFix = modelFromI-1;
                         }
 					}
 #				if 0
@@ -6597,13 +6597,13 @@
 				{
 				for (i=0; i<numCurrentDivisions; i++)
 					numVars[i] = NO;
-				foundEqual = YES;
+				modelFoundEqual = YES;
                 foundLeftPar = NO;
 				expecting = Expecting(ALPHA);
 				}
 			else if (expecting == Expecting(ALPHA))
 				{
-				if (foundEqual == YES)
+				if (modelFoundEqual == YES)
 					{
 					if (IsArgValid(tkn, tempStr) == NO_ERROR)
 						{
@@ -6618,7 +6618,7 @@
 						MrBayesPrint ("%s   Invalid Brlenspr argument\n", spacer);
 						return (ERROR);
 						}
-					foundEqual = NO;
+					modelFoundEqual = NO;
 					if (!strcmp(colonPr,"Fixed"))
 						expecting = Expecting(LEFTPAR);
 					else
@@ -6633,7 +6633,7 @@
 					    MrBayesPrint ("%s   Could not set fixed branch lengths from the user tree '%s'\n", spacer, tkn);
 					    return (ERROR);
 					    }
-                    fromI = tempInt + 1;        /* fromI is used to hold the index of the user tree, 1-based */
+                    modelFromI = tempInt + 1;        /* modelFromI is used to hold the index of the user tree, 1-based */
                     expecting = Expecting(RIGHTPAR);
                     foundLeftPar = NO;
                     }
@@ -6815,7 +6815,7 @@
 						MrBayesPrint ("%s   Tree needs to be in the range %d to %d\n", spacer, 1, numUserTrees);
 						return (ERROR);
 						}
-					fromI = tempInt;
+					modelFromI = tempInt;
 					expecting = Expecting(RIGHTPAR);
 					}
                 foundLeftPar = NO;
@@ -6837,20 +6837,20 @@
 		    		for (i=0; i<numCurrentDivisions; i++)
 			        	{
 			        	if (activeParts[i] == YES || nApplied == 0)
-				        	modelParams[i].brlensFix = fromI-1;
+				        	modelParams[i].brlensFix = modelFromI-1;
                         if (!strcmp(colonPr,"Fixed"))
                             {
 						    if (nApplied == 0 && numCurrentDivisions == 1)
-							    MrBayesPrint ("%s   Setting Brlenspr to Fixed(%s)\n", spacer, userTree[fromI-1]->name);
+							    MrBayesPrint ("%s   Setting Brlenspr to Fixed(%s)\n", spacer, userTree[modelFromI-1]->name);
 						    else
-							    MrBayesPrint ("%s   Setting Brlenspr to Fixed(%s) for partition %d\n", spacer, userTree[fromI-1]->name, i+1);
+							    MrBayesPrint ("%s   Setting Brlenspr to Fixed(%s) for partition %d\n", spacer, userTree[modelFromI-1]->name, i+1);
                             }
                         else
                             {
 						    if (nApplied == 0 && numCurrentDivisions == 1)
-							    MrBayesPrint ("%s   Setting Brlenspr to Fixed(%s)\n", spacer, userTree[fromI-1]->name);
+							    MrBayesPrint ("%s   Setting Brlenspr to Fixed(%s)\n", spacer, userTree[modelFromI-1]->name);
 						    else
-							    MrBayesPrint ("%s   Setting Brlenspr to Fixed(%s) for partition %d\n", spacer, userTree[fromI-1]->name, i+1);
+							    MrBayesPrint ("%s   Setting Brlenspr to Fixed(%s) for partition %d\n", spacer, userTree[modelFromI-1]->name, i+1);
                             }
                         }
 					}
@@ -7186,7 +7186,7 @@
 			{
 			if (expecting == Expecting(EQUALSIGN))
                 {
-                foundDash = NO;
+                modelFoundDash = NO;
 				expecting = Expecting(ALPHA);
                 }
 			else if (expecting == Expecting(ALPHA))
@@ -7216,15 +7216,15 @@
 				}
             else if (expecting == Expecting(DASH))
                 {
-                foundDash = YES;
+                modelFoundDash = YES;
                 expecting = Expecting(NUMBER);
                 }
             else if (expecting == Expecting(NUMBER))
 				{
 				sscanf (tkn, "%lf", &tempD);
-                if (foundDash == YES)
+                if (modelFoundDash == YES)
                     {
-                    foundDash = NO;
+                    modelFoundDash = NO;
                     tempD *= -1.0;
                     }
 				nApplied = NumActiveParts ();
@@ -7879,11 +7879,11 @@
 			if (expecting == Expecting(EQUALSIGN))
 				{
 				expecting = Expecting(ALPHA);
-				isNegative = NO;
+				modelIsNegative = NO;
 				}
 			else if (expecting == Expecting(ALPHA))
 				{
-				isNegative = NO;
+				modelIsNegative = NO;
 				if (IsArgValid(tkn, tempStr) == NO_ERROR)
 					{
 					nApplied = NumActiveParts ();
@@ -7909,7 +7909,7 @@
 			else if (expecting == Expecting(DASH))
 				{
 				expecting  = Expecting(NUMBER);
-				isNegative = YES;
+				modelIsNegative = YES;
 				}
 			else if (expecting == Expecting(NUMBER))
 				{
@@ -7921,7 +7921,7 @@
 						if (!strcmp(modelParams[i].growthPr,"Uniform"))
 							{
 							sscanf (tkn, "%lf", &tempD);
-							if (isNegative == YES)
+							if (modelIsNegative == YES)
 								tempD *= -1.0;
 							modelParams[i].growthUni[numVars[i]++] = tempD;
 							if (numVars[i] == 1)
@@ -7943,7 +7943,7 @@
 						else if (!strcmp(modelParams[i].growthPr,"Normal"))
 							{
 							sscanf (tkn, "%lf", &tempD);
-							if (isNegative == YES)
+							if (modelIsNegative == YES)
 								tempD *= -1.0;
 							modelParams[i].growthNorm[numVars[i]++] = tempD;
 							if (numVars[i] == 1)
@@ -7975,7 +7975,7 @@
 						else if (!strcmp(modelParams[i].growthPr,"Fixed"))
 							{
 							sscanf (tkn, "%lf", &tempD);
-							if (isNegative == YES)
+							if (modelIsNegative == YES)
 								tempD *= -1.0;
 							modelParams[i].growthFix = tempD;
 							if (nApplied == 0 && numCurrentDivisions == 1)
@@ -7986,7 +7986,7 @@
 							}
 						}
 					}
-				isNegative = NO;
+				modelIsNegative = NO;
 				}
 			else if (expecting == Expecting(COMMA))
 				{
@@ -8005,8 +8005,8 @@
 			if (expecting == Expecting(EQUALSIGN))
 				{
 				expecting = Expecting(ALPHA);
-				foundAaSetting = foundExp = modelIsFixed = foundDash = NO;
-				fromI = 0;
+				foundAaSetting = modelFoundExp = modelIsFixed = modelFoundDash = NO;
+				modelFromI = 0;
 				for (i=0; i<10; i++)
 					tempAaModelPrs[i] = 0.0;
 				}
@@ -8109,7 +8109,7 @@
 						{
 						if (IsSame ("Exponential", tkn) == SAME || IsSame ("Exponential", tkn) == CONSISTENT_WITH)
 							{
-							foundExp = YES;
+							modelFoundExp = YES;
 							expecting = Expecting(LEFTPAR);
 							}
 						else	
@@ -8124,24 +8124,24 @@
 			else if (expecting == Expecting(NUMBER))
 				{
 				sscanf (tkn, "%lf", &tempD);
-				if (fromI >= 10)
+				if (modelFromI >= 10)
 					{
 					MrBayesPrint ("%s   Too many arguments in Aamodelpr\n", spacer);
 					return (ERROR);
 					}
 				if (modelIsFixed == NO)
 					{
-					if (foundExp == YES)
+					if (modelFoundExp == YES)
 						{
-						if (foundDash == YES)
-							tempAaModelPrs[fromI++] = -tempD;
+						if (modelFoundDash == YES)
+							tempAaModelPrs[modelFromI++] = -tempD;
 						else
-							tempAaModelPrs[fromI++] = tempD;
+							tempAaModelPrs[modelFromI++] = tempD;
 						expecting  = Expecting(RIGHTPAR);
 						}
 					else
 						{
-						if (foundDash == YES)
+						if (modelFoundDash == YES)
 							{
 							MrBayesPrint ("%s   Unexpected \"-\" in Aamodelpr\n", spacer);
 							return (ERROR);
@@ -8149,13 +8149,13 @@
 						else
 							{
 							if (tempD <= 0.000000000001)
-								tempAaModelPrs[fromI++] = -1000000000;
+								tempAaModelPrs[modelFromI++] = -1000000000;
 							else
-								tempAaModelPrs[fromI++] = (MrBFlt) log(tempD);
+								tempAaModelPrs[modelFromI++] = (MrBFlt) log(tempD);
 							}
 						expecting  = Expecting(COMMA) | Expecting(RIGHTPAR);
 						}
-					foundDash = NO;
+					modelFoundDash = NO;
 					}
 				else
 					{
@@ -8169,7 +8169,7 @@
 					expecting  = Expecting(ALPHA);
 				else
 					{
-					if (foundExp == YES)
+					if (modelFoundExp == YES)
 						expecting  = Expecting(NUMBER) | Expecting(DASH);
 					else
 						expecting  = Expecting(NUMBER) | Expecting(ALPHA);
@@ -8181,14 +8181,14 @@
 					expecting = Expecting(PARAMETER) | Expecting(SEMICOLON);
 				else
 					{
-					if (foundExp == YES)
+					if (modelFoundExp == YES)
 						{
-						foundExp = NO;
+						modelFoundExp = NO;
 						expecting = Expecting(COMMA) | Expecting(RIGHTPAR);
 						}
 					else	
 						{
-						if (fromI < 10)
+						if (modelFromI < 10)
 							{
 							MrBayesPrint ("%s   Too few arguments in Aamodelpr\n", spacer);
 							return (ERROR);
@@ -8216,9 +8216,9 @@
 				}
 			else if (expecting == Expecting(DASH))
 				{
-				if (foundExp == YES)
+				if (modelFoundExp == YES)
 					{
-					foundDash = YES;
+					modelFoundDash = YES;
 					expecting  = Expecting(NUMBER);
 					}
 				else
@@ -8625,14 +8625,14 @@
 				{
 				for (i=0; i<numCurrentDivisions; i++)
 					activeParts[i] = NO;
-				fromI = toJ = -1;
-				foundDash = NO;
+				modelFromI = modelToJ = -1;
+				modelFoundDash = NO;
 				expecting = Expecting(NUMBER) | Expecting(ALPHA);
 				}
 			else if (expecting == Expecting(RIGHTPAR))
 				{
-				if (fromI != -1)
-					activeParts[fromI-1] = YES;
+				if (modelFromI != -1)
+					activeParts[modelFromI-1] = YES;
 				expecting = Expecting(PARAMETER) | Expecting(SEMICOLON);
 				}
 			else if (expecting == Expecting(COMMA))
@@ -8659,20 +8659,20 @@
 					MrBayesPrint ("%s   Partition delimiter is too large\n", spacer);
 					return (ERROR);
 					}
-				if (fromI == -1)
-					fromI = tempInt;
-				else if (fromI != -1 && toJ == -1 && foundDash == YES && foundComma == NO)
+				if (modelFromI == -1)
+					modelFromI = tempInt;
+				else if (modelFromI != -1 && modelToJ == -1 && modelFoundDash == YES && foundComma == NO)
 					{
-					toJ = tempInt;
-					for (i=fromI-1; i<toJ; i++)
+					modelToJ = tempInt;
+					for (i=modelFromI-1; i<modelToJ; i++)
 						activeParts[i] = YES;
-					fromI = toJ = -1;
-					foundDash = NO;
+					modelFromI = modelToJ = -1;
+					modelFoundDash = NO;
 					}
-				else if (fromI != -1 && toJ == -1 && foundDash == NO && foundComma == YES)
+				else if (modelFromI != -1 && modelToJ == -1 && modelFoundDash == NO && foundComma == YES)
 					{
-					activeParts[fromI-1] = YES;
-					fromI = tempInt;
+					activeParts[modelFromI-1] = YES;
+					modelFromI = tempInt;
 					foundComma = NO;
 					}
 					
@@ -8682,7 +8682,7 @@
 				}
 			else if (expecting == Expecting(DASH))
 				{
-				foundDash = YES;
+				modelFoundDash = YES;
 				expecting = Expecting(NUMBER);
 				}
 			else
@@ -9033,7 +9033,7 @@
     MrBFlt              minRate, maxRate, clockRate;
 	static Param	    *param = NULL;
 	static MrBFlt		*theValue, theValueMin, theValueMax;
-	static int			useSubvalues, useStdStateFreqs, useIntValues, numExpectedValues, nValuesRead, runIndex, chainIndex, foundName, foundDash;
+	static int			useSubvalues, useStdStateFreqs, useIntValues, numExpectedValues, nValuesRead, runIndex, chainIndex, foundName, modelFoundDash;
 	static char			*tempName=NULL;
 
 	if (defMatrix == NO)
@@ -9068,7 +9068,7 @@
 			useSubvalues = NO;
             useIntValues = NO;
             useStdStateFreqs = NO;
-			foundComma = foundEqual = foundName = foundDash = NO;
+			foundComma = modelFoundEqual = foundName = modelFoundDash = NO;
 			expecting = Expecting(LEFTCURL) | Expecting(LEFTPAR) | 	Expecting(EQUALSIGN);
 			}
 		else
@@ -9328,7 +9328,7 @@
 		}
 	else if (expecting == Expecting(LEFTPAR))
 		{
-		if (foundEqual == NO)
+		if (modelFoundEqual == NO)
 			{
 			foundName = YES;	/* we found the name */
 			/* we will be reading in run and chain indices */
@@ -9342,7 +9342,7 @@
 		}
     else if (expecting == Expecting(DASH))
         {
-        foundDash = YES;
+        modelFoundDash = YES;
         expecting = Expecting(NUMBER);
         }
 	else if (expecting == Expecting(NUMBER))
@@ -9353,7 +9353,7 @@
 			SafeStrcat (&tempName, tkn);
 			expecting = Expecting(COMMA) | Expecting(LEFTPAR) | Expecting(RIGHTCURL) | Expecting(EQUALSIGN);
 			}
-		else if (foundEqual == YES)
+		else if (modelFoundEqual == YES)
 			{
             theValueMin = param->min;
             theValueMax = param->max;
@@ -9411,13 +9411,13 @@
 			    sscanf (tkn, "%d", &tempInt);
 			else
                 sscanf (tkn, "%lf", &tempFloat);
-            if (foundDash == YES)
+            if (modelFoundDash == YES)
                 {
                 if (useIntValues == NO)
                     tempFloat = -tempFloat;
                 else
                     tempInt = -tempInt;
-                foundDash = NO;
+                modelFoundDash = NO;
                 }
 			if (useIntValues == NO && (tempFloat < theValueMin || tempFloat > theValueMax))
 				{
@@ -9463,7 +9463,7 @@
 				}
 			expecting = Expecting (COMMA) | Expecting(RIGHTPAR);
 			}
-		else /* if (foundEqual == NO) */
+		else /* if (modelFoundEqual == NO) */
 			{
 			sscanf (tkn, "%d", &tempInt);
 			if (foundComma == NO)
@@ -9491,12 +9491,12 @@
 		}
 	else if (expecting == Expecting(COMMA))
 		{
-		if (foundEqual == YES)
+		if (modelFoundEqual == YES)
 			{
 			/* we expect another parameter value */
 			expecting = Expecting(NUMBER);
 			}
-		else /* if (foundEqual == NO) */
+		else /* if (modelFoundEqual == NO) */
 			{
 			/* we will be reading in chain index, if present */
 			foundComma = YES;
@@ -9508,12 +9508,12 @@
 		}
 	else if (expecting == Expecting(RIGHTPAR))
 		{
-		if (foundEqual == NO)
+		if (modelFoundEqual == NO)
 			{
 			/* this is the end of the run and chain specification */
 			expecting = Expecting(EQUALSIGN);
 			}
-		else /* if (foundEqual == YES) */
+		else /* if (modelFoundEqual == YES) */
 			{
 			/* this is the end of the parameter values */
 			if (nValuesRead != numExpectedValues)
@@ -9549,7 +9549,7 @@
 		}
 	else if (expecting == Expecting(EQUALSIGN))
 		{
-		foundEqual = YES;
+		modelFoundEqual = YES;
 		foundName = YES;
 
 		/* we now know that the name is complete; try to find the parameter with this name (case insensitive) */
@@ -19878,28 +19878,50 @@
     mt->Autotune = &AutotuneMultiplier;
     mt->targetRate = 0.25;
 
-    	/***************************			Begin Code added by Jeremy Brown 		*************************/
-
-	/* Move_TreeLen */
-	mt = &moveTypes[i++];
-	mt->name = "Whole treelength hit with multiplier";
-	mt->shortName = "TLMultiplier";
-	mt->tuningName[0] = "Multiplier tuning parameter";
-	mt->shortTuningName[0] = "lambda";	
-	mt->applicableTo[0] = BRLENS_UNI;
-	mt->applicableTo[1] = BRLENS_EXP;
-	mt->nApplicable = 2;
-	mt->moveFxn = &Move_TreeLen;
-	mt->relProposalProb = 2.0;
-	mt->numTuningParams = 1;
-	mt->tuningParam[0] = 2.0 * log (2.0);  /* lambda */
-	mt->minimum[0] = 0.00001;
-	mt->maximum[0] = 10000000.0;
-	mt->parsimonyBased = NO;
-	mt->level = STANDARD_USER;
-    mt->Autotune = &AutotuneMultiplier;
-    mt->targetRate = 0.25;
-
+    	/***************************			Begin Code added by Jeremy Brown 		*************************/
+
+
+
+	/* Move_TreeLen */
+
+	mt = &moveTypes[i++];
+
+	mt->name = "Whole treelength hit with multiplier";
+
+	mt->shortName = "TLMultiplier";
+
+	mt->tuningName[0] = "Multiplier tuning parameter";
+
+	mt->shortTuningName[0] = "lambda";	
+
+	mt->applicableTo[0] = BRLENS_UNI;
+
+	mt->applicableTo[1] = BRLENS_EXP;
+
+	mt->nApplicable = 2;
+
+	mt->moveFxn = &Move_TreeLen;
+
+	mt->relProposalProb = 2.0;
+
+	mt->numTuningParams = 1;
+
+	mt->tuningParam[0] = 2.0 * log (2.0);  /* lambda */
+
+	mt->minimum[0] = 0.00001;
+
+	mt->maximum[0] = 10000000.0;
+
+	mt->parsimonyBased = NO;
+
+	mt->level = STANDARD_USER;
+
+    mt->Autotune = &AutotuneMultiplier;
+
+    mt->targetRate = 0.25;
+
+
+
 	/***************************			End Code added by Jeremy Brown 		*************************/
 
 	/* Move_UnrootedSlider */