diff --git a/alignment/substitution.cpp b/alignment/substitution.cpp
index 953f41ae9..81f62681e 100644
--- a/alignment/substitution.cpp
+++ b/alignment/substitution.cpp
@@ -23,7 +23,7 @@ Substitution::Substitution(const std::string& sub_str, Alignment* const aln, con
         outError("Failed to parse the predefined mutation: '" + sub_str + "'. The new state is invalid.");
     
     // Parse the position
-    position = convert_int(sub_str.substr(num_sites_per_state, input_length - (num_sites_per_state + num_sites_per_state)).c_str()) - 1;
+    position = convert_int(sub_str.substr(num_sites_per_state, input_length - (num_sites_per_state + num_sites_per_state)).c_str()) - Params::getInstance().site_starting_index;
     if (aln->seq_type == SEQ_CODON)
         position = position * ONE_THIRD;
     
diff --git a/main/alisim.cpp b/main/alisim.cpp
index d5ebc313f..d9d37e549 100644
--- a/main/alisim.cpp
+++ b/main/alisim.cpp
@@ -364,7 +364,7 @@ std::vector<std::pair<std::string,std::string>> readMutations(const std::string&
             }
             // if not found -> all characters are spaces -> invalid
             else
-                outError("Invalid format '" + line + "'. Expected format should be <node_name><spaces><old_state><site><new_state>");
+                outError("Invalid format '" + line + "'. Expected format should be <node_name><spaces><list_of_mutations>");
             
             // remove spaces at the ending of the line
             pos = line.find_last_not_of(" ");
@@ -377,11 +377,11 @@ std::vector<std::pair<std::string,std::string>> readMutations(const std::string&
             }
             // if not found -> all characters are spaces -> invalid
             else
-                outError("Invalid format '" + line + "'. Expected format should be <node_name><spaces><old_state><site><new_state>");
+                outError("Invalid format '" + line + "'. Expected format should be <node_name><spaces><list_of_mutations>");
             
-            // validate the input format <node_name><spaces><old_state><site><new_state>
+            // validate the input format <node_name><spaces><list_of_mutations>
             if (line.length() < 5)
-                outError("Invalid format '" + line + "'. Expected format should be <node_name><spaces><old_state><site><new_state>");
+                outError("Invalid format '" + line + "'. Expected format should be <node_name><spaces><list_of_mutations>");
             
             // replace \t by a space
             line = regex_replace(line, std::regex("\t"), " ");
@@ -397,7 +397,7 @@ std::vector<std::pair<std::string,std::string>> readMutations(const std::string&
                 transform(node_name.begin(), node_name.end(), node_name.begin(), ::toupper);
             }
             else
-                outError("Invalid format '" + line + "'. Expected format should be <node_name><spaces><old_state><site><new_state>");
+                outError("Invalid format '" + line + "'. Expected format should be <node_name><spaces><list_of_mutations>");
             
             // get mutation list at that node
             std::string mutation_str = "";
@@ -408,7 +408,7 @@ std::vector<std::pair<std::string,std::string>> readMutations(const std::string&
             if (line.length() - pos)
                 mutation_str = line.substr(pos, line.length() - pos);
             else
-                outError("Invalid format '" + line + "'. Expected format should be <node_name><spaces><old_state><site><new_state>");
+                outError("Invalid format '" + line + "'. Expected format should be <node_name><spaces><list_of_mutations>");
             
             // record the mutations at that node
             node_mutations.push_back(std::pair<std::string,std::string>(node_name, mutation_str));
@@ -646,7 +646,7 @@ void getLockedSites(Node* const node, Node* const dad, std::vector<bool>* const
                 // vailidate position
                 if (pos >= seq_length)
                 {
-                    outWarning("Ignore a predefined mutation " + aln->convertStateBackStr(mut_it->getOldState()) + convertIntToString((aln->seq_type == SEQ_CODON ? pos * 3 : pos) + 1) + aln->convertStateBackStr(mut_it->getNewState()) + ". Position exceeds the sequence length " + convertIntToString(aln->seq_type == SEQ_CODON ? seq_length * 3 : seq_length));
+                    outWarning("Ignore a predefined mutation " + aln->convertStateBackStr(mut_it->getOldState()) + convertIntToString((aln->seq_type == SEQ_CODON ? pos * 3 : pos) + Params::getInstance().site_starting_index) + aln->convertStateBackStr(mut_it->getNewState()) + ". Position exceeds the sequence length " + convertIntToString(aln->seq_type == SEQ_CODON ? seq_length * 3 : seq_length));
                 }
                 // mark the site as locked
                 else
diff --git a/simulator/alisimulator.cpp b/simulator/alisimulator.cpp
index f522d7afa..2d701472e 100644
--- a/simulator/alisimulator.cpp
+++ b/simulator/alisimulator.cpp
@@ -1591,12 +1591,12 @@ void AliSimulator::handlePreMutations(const NeighborVec::iterator& it, int& pred
             {
                 // show infor
                 if (verbose_mode >= VB_MED)
-                    std::cout << "Apply a predefined mutation " << tree->aln->convertStateBackStr(mut_it->getOldState()) << convertIntToString(mut_it->getPosition() * num_sites_per_state + 1) << tree->aln->convertStateBackStr(mut_it->getNewState()) << std::endl;
+                    std::cout << "Apply a predefined mutation " << tree->aln->convertStateBackStr(mut_it->getOldState()) << convertIntToString(mut_it->getPosition() * num_sites_per_state + params->site_starting_index) << tree->aln->convertStateBackStr(mut_it->getNewState()) << std::endl;
                 
                 // if the old state is different from the one observed at the specified position -> show a warning
                 if ((*node_seq_chunk)[relative_pos] != mut_it->getOldState())
                 {
-                    outWarning("State " + tree->aln->convertStateBackStr(mut_it->getOldState()) + " is not observed at position/site " + convertIntToString(mut_it->getPosition() * num_sites_per_state + 1) + ", we observe state " + tree->aln->convertStateBackStr((*node_seq_chunk)[relative_pos]) + " instead.");
+                    outWarning("State " + tree->aln->convertStateBackStr(mut_it->getOldState()) + " is not observed at position/site " + convertIntToString(mut_it->getPosition() * num_sites_per_state + params->site_starting_index) + ", we observe state " + tree->aln->convertStateBackStr((*node_seq_chunk)[relative_pos]) + " instead.");
                 }
                 
                 // apply the substitution
@@ -1608,7 +1608,7 @@ void AliSimulator::handlePreMutations(const NeighborVec::iterator& it, int& pred
                 // write log - for debugging only
                 /*ofstream myfile;
                  myfile.open ("thread_" + convertIntToString(omp_get_thread_num()) + ".txt", std::ostream::app);
-                 myfile << tree->aln->convertStateBackStr(mut_it->getOldState()) << mut_it->getPosition() + 1 << tree->aln->convertStateBackStr(mut_it->getNewState())<< std::endl;
+                 myfile << tree->aln->convertStateBackStr(mut_it->getOldState()) << mut_it->getPosition() + params->site_starting_index << tree->aln->convertStateBackStr(mut_it->getNewState())<< std::endl;
                  myfile.close();*/
             }
         }
diff --git a/utils/tools.cpp b/utils/tools.cpp
index c36f6af97..0ccbf1aa3 100644
--- a/utils/tools.cpp
+++ b/utils/tools.cpp
@@ -1487,6 +1487,7 @@ void parseArg(int argc, char *argv[], Params &params) {
     params.alignment_id = 0;
     params.include_pre_mutations = false;
     params.mutation_file = "";
+    params.site_starting_index = 0;
     
     // store original params
     for (cnt = 1; cnt < argc; cnt++) {
@@ -5267,6 +5268,12 @@ void parseArg(int argc, char *argv[], Params &params) {
                 continue;
             }
             
+            if (strcmp(argv[cnt], "--index-from-one") == 0) {
+                params.site_starting_index = 1;
+                
+                continue;
+            }
+            
             if (strcmp(argv[cnt], "--distribution") == 0) {
                 cnt++;
                 if (cnt >= argc || argv[cnt][0] == '-')
diff --git a/utils/tools.h b/utils/tools.h
index e1d3fc716..4feccba8c 100644
--- a/utils/tools.h
+++ b/utils/tools.h
@@ -2601,6 +2601,11 @@ class Params {
     *  Mutation file that specifies pre-defined mutations occurs at nodes
     */
     std::string mutation_file;
+    
+    /**
+    *  site starting index (for predefined mutations in AliSim)
+    */
+    int site_starting_index;
 };
 
 /**