diff --git a/src/beast/app/tools/SATreeTraceAnalysis.java b/src/beast/app/tools/SATreeTraceAnalysis.java
index 1801dee..4a2aec6 100644
--- a/src/beast/app/tools/SATreeTraceAnalysis.java
+++ b/src/beast/app/tools/SATreeTraceAnalysis.java
@@ -18,7 +18,6 @@
  */
 
 public class SATreeTraceAnalysis extends TreeTraceAnalysis {
-
     FrequencySet<String> pairs = new FrequencySet<String>();
 
     public SATreeTraceAnalysis(List<Tree> posteriorTreeList, double burninFraction) {
@@ -79,7 +78,7 @@ public List<String> getNewickTrees () {
      * @return a report string
      * @throws Exception
      */
-	public String toReportString(boolean printCladeFrequencies, boolean printPairs, boolean printFrequencies, boolean printTopologyCredibleSet, boolean isHTML) throws Exception {
+	public String toReportString(boolean printCladeFrequencies, boolean printPairs, boolean printFrequencies, boolean printTopologyCredibleSet, Double credSetProbability, boolean isHTML) throws Exception {
         FrequencySet<String> clades = new FrequencySet<String>();
         ArrayList<String> tmp = new ArrayList<String>();
 
@@ -168,7 +167,7 @@ public String toReportString(boolean printCladeFrequencies, boolean printPairs,
         }
 
         if (printTopologyCredibleSet) {
-            countTopologies(output);
+            countTopologies(output, credSetProbability);
         }
 
         ps.flush();
@@ -324,8 +323,9 @@ public FrequencySet<String> countSAFrequencies(boolean print, boolean useRanking
     /**
      *
      */
-    public void countTopologies(ResultsOutput output) {
+    public void countTopologies(ResultsOutput output, Double credSetProbability) {
         FrequencySet<String> topologies = new FrequencySet<String>();
+        topologies.setCredSetProbability(credSetProbability);
         List<String> trees;
         trees = getNewickTrees(true);
 
diff --git a/src/beast/app/tools/SampledAncestorTreeAnalyser.java b/src/beast/app/tools/SampledAncestorTreeAnalyser.java
index 68aef12..6a95c70 100644
--- a/src/beast/app/tools/SampledAncestorTreeAnalyser.java
+++ b/src/beast/app/tools/SampledAncestorTreeAnalyser.java
@@ -33,19 +33,25 @@ public class SampledAncestorTreeAnalyser extends beast.core.Runnable {
 	private Boolean printCladeFrequencies = false;
 	private Boolean printTopologyCredibleSet = false;
 	private Boolean toStandardOutput = true;
+	private Double credibleSetProportion = 0.95;
+	private Double burninProportion = 0.1;
 
 	public SampledAncestorTreeAnalyser() {}
 	public SampledAncestorTreeAnalyser(@Param(name="file", description="tree file containing set of ancestral ancestor trees") File file,
+			@Param(name="burnin", description="percentage of trees to be discarded as burn-in", defaultValue="10.0") Double burninPercentage,
 			@Param(name="printFrequencies", description="show sampled ancestor frequencies in output table", defaultValue="true") Boolean printFrequencies,
 			@Param(name="printPairs", description="show ancestor-descendant pair frequencies in output table", defaultValue="false") Boolean printPairs,
 			@Param(name="printCladeFrequencies", description="show sampled ancestor clade frequencies in output table", defaultValue="false") Boolean printCladeFrequencies,
 			@Param(name="printTopologyCredibleSet", description="show sampled ancestor tree topology frequencies in output table", defaultValue="false") Boolean printTopologyCredibleSet,
+			@Param(name="credibleSet", description="percent coverage of the credible set (used for printTopologyCredibleSet)", defaultValue="95.0") Double credibleSetPercentage,
 			@Param(name="toStandardOutput", description="print to standard output", defaultValue="true") Boolean toStdOut) {
 		this.file = file;
+		this.burninProportion = burninPercentage / 100.0;
 		this.printFrequencies = printFrequencies;
 		this.printPairs = printPairs;
 		this.printCladeFrequencies = printCladeFrequencies;
 		this.printTopologyCredibleSet = printTopologyCredibleSet;
+		this.credibleSetProportion = credibleSetPercentage / 100.0;
 		this.toStandardOutput = toStdOut;
 	}
 
@@ -87,7 +93,23 @@ public Boolean getPrintTopologyCredibleSet() {
 	public void setPrintTopologyCredibleSet(Boolean printTopologyCredibleSet) {
 		this.printTopologyCredibleSet = printTopologyCredibleSet;
 	}
+
+	public Double getBurnin() {
+		return this.burninProportion * 100.0;
+	}
 	
+	public void setBurnin(Double burnin) {
+		this.burninProportion = burnin / 100.0;
+	}
+
+	public Double getCredibleSet() {
+		return this.credibleSetProportion * 100.0;
+	}
+
+	public void setCredibleSet(Double credibleSet) {
+		this.credibleSetProportion = credibleSet / 100.0;
+	}
+
 	public void run() throws Exception {
  
         FileReader reader = null;
@@ -96,9 +118,9 @@ public void run() throws Exception {
             System.out.println("Reading file " + file.getName());
             reader = new FileReader(file);
             List<Tree> trees = SATreeTraceAnalysis.Utils.getTrees(file);
-            SATreeTraceAnalysis analysis = new SATreeTraceAnalysis(trees, 0.1);
+            SATreeTraceAnalysis analysis = new SATreeTraceAnalysis(trees, burninProportion);
 
-			String result = analysis.toReportString(printCladeFrequencies, printPairs, printFrequencies, printTopologyCredibleSet, !toStandardOutput);
+			String result = analysis.toReportString(printCladeFrequencies, printPairs, printFrequencies, printTopologyCredibleSet, credibleSetProportion, !toStandardOutput);
 
 			if (toStandardOutput) {
 				System.out.println(result);