diff --git a/alignment.cpp b/alignment.cpp
index a0a27a6c..0b04a128 100644
--- a/alignment.cpp
+++ b/alignment.cpp
@@ -763,8 +763,22 @@ SeqType Alignment::detectSequenceType(StrVector &sequences) {
         }
     if (((double)num_nuc) / num_ungap > 0.9)
         return SEQ_DNA;
-    if (((double)num_bin) / num_ungap > 0.9)
-        return SEQ_BINARY;
+    if (((double)num_bin) / num_ungap > 0.9) {
+        cout << "[BINARY-SEQUENCE-WARNING]" << endl;
+        cout << "Since the PLL library we are using only supports sequence of type DNA, the following process will treat the input as DNA (mapping 0 to A and 1 to G) and not break the property of resulting trees." << endl;
+        cout << "[BINARY-SEQUENCE-WARNING]" << endl;
+        cout << endl;
+
+        for (StrVector::iterator it = sequences.begin(); it != sequences.end(); it++) {
+            for (string::iterator i = it->begin(); i != it->end(); i++) {
+                if ((*i) == '0') *i = 'A';
+                if ((*i) == '1') *i = 'G';
+                if ((*i) == '-') *i = 'R';
+            }
+        }
+
+        return SEQ_DNA;
+    }
     if (((double)num_alpha) / num_ungap > 0.9)
         return SEQ_PROTEIN;
     if (((double)(num_alpha+num_digit)) / num_ungap > 0.9)
diff --git a/phyloanalysis.cpp b/phyloanalysis.cpp
index 3b825adc..b63a20c0 100644
--- a/phyloanalysis.cpp
+++ b/phyloanalysis.cpp
@@ -2130,6 +2130,10 @@ void runPhyloAnalysis(Params &params) {
 	IQTree *tree;
 
 	/****************** read in alignment **********************/
+	if (strcmp(params.sequence_type, "BIN") == 0) {
+		params.sequence_type = "DNA";
+	}
+
 	if (params.partition_file) {
 		// Partition model analysis
 		if(params.partition_type){
@@ -2159,8 +2163,6 @@ void runPhyloAnalysis(Params &params) {
 			alignment = aln;
 		}
 		tree = new IQTree(alignment);
-
-
 	}
 
 //	if(params.maximum_parsimony && (params.gbo_replicates || params.sankoff_cost_file)){