diff --git a/src/snap/Data.java b/src/snap/Data.java
index 94ef213..08797b1 100644
--- a/src/snap/Data.java
+++ b/src/snap/Data.java
@@ -36,6 +36,7 @@
 import beast.base.core.Input;
 import beast.base.core.ProgramStatus;
 import beast.base.core.Input.Validate;
+import beast.base.core.Log;
 import beast.base.evolution.alignment.Sequence;
 import beast.base.evolution.alignment.Taxon;
 import beast.base.evolution.alignment.TaxonSet;
@@ -125,6 +126,13 @@ public void initAndValidate() {
 			} else if (rawDataType instanceof Nucleotide) {
 				// call SNPs by setting first sequence to all zero
 				// any character in subsequent sequences that is not the same will be set to one
+				Log.warning("=====================================================================");
+				Log.warning("WARNING: Calling SNPs by setting the first sequence to be all zero  ");
+				Log.warning("WARNING: This may not be appropriate if your data has more than two ");
+				Log.warning("WARNING: states on a site and the first sequence has a low frequency");
+				Log.warning("WARNING: state.");
+				Log.warning("=====================================================================");
+
 				String refferenceSeq = sequences.get(0).dataInput.get().replaceAll("\\s", "");
 				
 				for(TaxonSet set : m_taxonsets.get()) {
diff --git a/src/snap/app/inputeditor/DataInputEditor.java b/src/snap/app/inputeditor/DataInputEditor.java
index 7fa557e..8da04ef 100644
--- a/src/snap/app/inputeditor/DataInputEditor.java
+++ b/src/snap/app/inputeditor/DataInputEditor.java
@@ -11,7 +11,9 @@
 import beastfx.app.inputeditor.BeautiDoc;
 import beastfx.app.inputeditor.GuessPatternDialog;
 import beastfx.app.inputeditor.InputEditor;
+import beastfx.app.util.Alert;
 import beastfx.app.util.FXUtils;
+import javafx.application.Platform;
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
 import javafx.event.EventHandler;
@@ -34,6 +36,7 @@
 import beast.base.evolution.alignment.Sequence;
 import beast.base.evolution.alignment.Taxon;
 import beast.base.evolution.alignment.TaxonSet;
+import beast.base.evolution.datatype.Nucleotide;
 
 
 
@@ -76,6 +79,15 @@ public void setTaxon2(String taxon2) {
 	String m_sFilter = ".*";
 	int m_sortByColumn = 0;
 	boolean m_bIsAscending = true;
+
+	private static boolean firstNucleotideOccurance = false;
+	private final static String nucleotideMessage = 
+			"A nucleotide alignment was loaded and SNPs will be called by setting the first "
+			+ "sequence as all zeros and other sequences as 1 when they differ from the first sequence.\n\n"
+			+ "This could lead to problems if you have sites with more than two values and the first sequence "
+			+ "contains a low frequency state.\n\n"
+			+ "Consider using phrynomics or other tools to preprocess your alignment instead of using the"
+			+ "raw nucleotide alignment.";
 	
 	@Override
 	public Class<?> type() {
@@ -86,6 +98,16 @@ public Class<?> type() {
 	@Override
 	public void init(Input<?> input, BEASTInterface plugin, int itemNr, ExpandOption bExpand, boolean bAddButtons) {
 		m_input = input;
+		
+		if (!firstNucleotideOccurance) {
+			snap.Data data = (snap.Data) m_input.get();
+			Alignment rawdata = data.m_rawData.get();
+			if (rawdata.getDataType() instanceof Nucleotide) {
+				Platform.runLater(() -> Alert.showMessageDialog(this, nucleotideMessage));
+				firstNucleotideOccurance = true;	
+			}
+		}
+
 		m_beastObject = plugin;
 		this.itemNr = itemNr;
 		List<TaxonSet> taxonset = ((snap.Data)input.get()).m_taxonsets.get(); 
@@ -332,13 +354,17 @@ void parseTrait(String trait) {
 		List<Taxon> taxa = new ArrayList<Taxon>();
         for (Alignment alignment : getDoc().alignments) {
             for (Sequence sequence : alignment.sequenceInput.get()) {
-				Taxon taxon = new Taxon();
-				// ensure sequence and taxon do not get same ID
-				if (sequence.getID() == null || sequence.getID().equals(sequence.taxonInput.get())) {
-					sequence.setID("_"+sequence.getID());
-				}
-				taxon.setID(sequence.taxonInput.get());
-				taxa.add(taxon);
+            	if (!doc.taxaset.containsKey(sequence.taxonInput.get())) {
+					Taxon taxon = new Taxon();
+					// ensure sequence and taxon do not get same ID
+					if (sequence.getID() == null || sequence.getID().equals(sequence.taxonInput.get())) {
+						sequence.setID("_"+sequence.getID());
+					}
+					taxon.setID(sequence.taxonInput.get());
+					taxa.add(taxon);
+					doc.addPlugin(taxon);
+            	}
+        		taxa.add(doc.taxaset.get(sequence.taxonInput.get()));
             }
 		}
 		HashMap<String, TaxonSet> map = new HashMap<String, TaxonSet>();
@@ -484,6 +510,7 @@ private void modelToTaxonset() {
 				TaxonSet taxonset = new TaxonSet();
 				taxonset.setID(sTaxonSetID);
 				m_taxonset.add(taxonset);
+				doc.addPlugin(taxonset);
 			}
 			m_taxonMap.put(sLineageID, sTaxonSetID);
 		}