diff --git a/README.md b/README.md
new file mode 100644
index 0000000..0b37b0b
--- /dev/null
+++ b/README.md
@@ -0,0 +1,47 @@
+# MiMi
+
+```
+  ／l、    	.  . .  .
+（ﾟ､ ｡ ７    	|\/|*|\/|*
+  l  ~ヽ    	|  |||  ||
+  じしf_,)ノ	|  |||  ||
+
+Morphology into Molecules into
+GPL	Guoyi	Zhang,	2023
+```
+
+## Functions
+
+Convert any formats listed in `Accepted formats` to each other.
+
+## Arguments
+
+- -h	--help;
+
+- -i	--input		${filename};
+
+- -o	--output	${filename};
+
+## Accepted formats
+
+- fas	fasta
+
+- nex	nexus
+
+- phy	phylip
+
+- tnt	ss
+
+## Compile
+
+```
+g++ main.cpp -o mimi
+```
+
+## License
+
+You should note that the license is (GPL)[https://www.gnu.org/licenses/gpl-3.0.html].
+
+## Acknowledgements
+
+Thanks to my beloved daughter MiMi (Ragdoll cat) for accompanying me in my life, mom loves you forever.
diff --git a/main.cpp b/main.cpp
index 81ce952..caa6ac5 100644
--- a/main.cpp
+++ b/main.cpp
@@ -1,33 +1,30 @@
-#include <iostream>
-#include <fstream>
-#include <sstream> 
-#include <string>
 #include <algorithm>
+#include <fstream>
+#include <iostream>
+#include <sstream>
+#include <string>
 
 using namespace std;
 
-class Basic_arg{
-public:
-	int intype=0, outype=0;
-	char *itn, *otn;
-	Basic_arg(int intype, int outype, char* itn, char *otn):
-		intype(intype), outype(outype),
-		itn(itn), otn(otn)
-	{}; 
+class Basic_arg {
+ public:
+  int intype = 0, outype = 0;
+  char *itn, *otn;
+  Basic_arg(int intype, int outype, char* itn, char* otn)
+      : intype(intype), outype(outype), itn(itn), otn(otn){};
 };
 
 class Sample {
-public:
-	unsigned ntax, nchar;
-	string *taxas, *chars;
-	Sample(unsigned ntax, unsigned nchar):
-       		ntax(ntax), nchar(nchar) {
-			taxas = new string[ntax];
-			chars = new string[ntax];
-		};
+ public:
+  unsigned ntax, nchar;
+  string *taxas, *chars;
+  Sample(unsigned ntax, unsigned nchar) : ntax(ntax), nchar(nchar) {
+    taxas = new string[ntax];
+    chars = new string[ntax];
+  };
 };
 
-Basic_arg procargs (int nargs, char ** arg, char* itn, char* otn);
+Basic_arg procargs(int nargs, char** arg, char* itn, char* otn);
 Sample read_input(char* itn, int intype);
 void show_help(int help_num);
 Sample readFas(char* itn);
@@ -46,54 +43,57 @@ string add_space(char x, string str_old);
 string checktype(string str);
 int countfre(string str, char c);
 int checkextension(string str);
-	
-Sample readPhy(char* itn){
-  //read file
+
+Sample readPhy(char* itn) {
+  // read file
   ifstream matrixfile;
   matrixfile.open(itn);
-  //read number of taxa and charcter
+  // read number of taxa and charcter
   string sntax, snseq, snall;
-  getline(matrixfile,snall);
-  istringstream istr(snall); 
-  istr >> sntax; istr >> snseq;
+  getline(matrixfile, snall);
+  istringstream istr(snall);
+  istr >> sntax;
+  istr >> snseq;
   int ntax, nchar;
-  ntax = stoi (sntax); nchar = stoi (snseq); // string to int
-  Sample sam(ntax, nchar);   
-  //read sequence
+  ntax = stoi(sntax);
+  nchar = stoi(snseq);  // string to int
+  Sample sam(ntax, nchar);
+  // read sequence
   int lennum;
-  for(lennum=0;lennum<sam.ntax;lennum++){
-    getline(matrixfile,snall);
+  for (lennum = 0; lennum < sam.ntax; lennum++) {
+    getline(matrixfile, snall);
     istringstream istr(snall);
-    istr >> sam.taxas[lennum]; istr >> sam.chars[lennum];
+    istr >> sam.taxas[lennum];
+    istr >> sam.chars[lennum];
   }
   matrixfile.close();
   // return to class
   return sam;
 }
 
-Sample readFas(char* itn){
+Sample readFas(char* itn) {
   int ntax, nchar, lnum;
   ifstream matrixfile;
   matrixfile.open(itn);
   // check line number and taxa number
   ntax = 0;
   string temln;
-  for(lnum=0;getline(matrixfile,temln);lnum++){
-    if(temln[0]=='>'){
+  for (lnum = 0; getline(matrixfile, temln); lnum++) {
+    if (temln[0] == '>') {
       ntax++;
     }
   }
   matrixfile.clear();
   matrixfile.seekg(0);
   // check the nchar
-  string *str_a = new string;
-  string *str_b = new string;
-  int r = lnum/ntax;
-  for (int i=0; i<r;i++){
+  string* str_a = new string;
+  string* str_b = new string;
+  int r = lnum / ntax;
+  for (int i = 0; i < r; i++) {
     getline(matrixfile, *str_a);
-    if(i>0){
-       *str_b = *str_b + *str_a; 
-    } 
+    if (i > 0) {
+      *str_b = *str_b + *str_a;
+    }
   }
   nchar = (*str_b).length();
   delete str_a;
@@ -105,183 +105,192 @@ Sample readFas(char* itn){
   // create class
   Sample sam(ntax, nchar);
   // get class
-  string *str_c = new string;
-  for (int a=1, b=0;a<=lnum;a++){
-    if(a%r==1){
-      getline(matrixfile,sam.taxas[b]);
-      sam.taxas[b].erase(0,1);  
+  string* str_c = new string;
+  for (int a = 1, b = 0; a <= lnum; a++) {
+    if (a % r == 1) {
+      getline(matrixfile, sam.taxas[b]);
+      sam.taxas[b].erase(0, 1);
     }
-    if(a%r>1){
-      getline(matrixfile,*str_c);
+    if (a % r > 1) {
+      getline(matrixfile, *str_c);
       sam.chars[b] = sam.chars[b] + *str_c;
     }
-    if(a%r==0){
-      getline(matrixfile,*str_c);
+    if (a % r == 0) {
+      getline(matrixfile, *str_c);
       sam.chars[b] = sam.chars[b] + *str_c;
       b++;
-    }   
+    }
   }
   delete str_c;
-  str_c = nullptr; 
+  str_c = nullptr;
   matrixfile.close();
   return sam;
 }
 
-Sample readTnt(char* itn){
+Sample readTnt(char* itn) {
   int ntax, nchar;
   ifstream matrixfile;
   matrixfile.open(itn);
   // get nchar and ntax
   string stri, sntax, snchar;
-  for(int i=0;i<1;){
-      getline(matrixfile,stri);
-      istringstream istr(stri); 
-      istr >> snchar; istr >> sntax;
-      if(isNum(sntax) && isNum(snchar)){
-              ntax=stoi(sntax);
-	      nchar=stoi(snchar);
-	      i++;
-      }
+  for (int i = 0; i < 1;) {
+    getline(matrixfile, stri);
+    istringstream istr(stri);
+    istr >> snchar;
+    istr >> sntax;
+    if (isNum(sntax) && isNum(snchar)) {
+      ntax = stoi(sntax);
+      nchar = stoi(snchar);
+      i++;
+    }
   }
   // create class
-  Sample sam(ntax,nchar);
+  Sample sam(ntax, nchar);
   // get class
   int lennum;
-  for(lennum=0;lennum<sam.ntax;lennum++){
-    getline(matrixfile,stri);
+  for (lennum = 0; lennum < sam.ntax; lennum++) {
+    getline(matrixfile, stri);
     istringstream istr(stri);
-    istr >> sam.taxas[lennum]; istr >> sam.chars[lennum];
+    istr >> sam.taxas[lennum];
+    istr >> sam.chars[lennum];
   }
   matrixfile.close();
   return sam;
 }
 
 bool isNum(string strnum) {
-	char* p;
-	strtol(strnum.c_str(), &p, 10);
-	return *p == 0;
+  char* p;
+  strtol(strnum.c_str(), &p, 10);
+  return *p == 0;
 }
 
-Sample readNex(char* itn){
+Sample readNex(char* itn) {
   int ntax, nchar;
-  // open file 
+  // open file
   ifstream matrixfile;
   matrixfile.open(itn);
-  // some tem 
+  // some tem
   string snall, stri, str_a, str_b;
-  bool found = false, found_ntax = false, found_nchar = false, found_equal = false;
+  bool found = false, found_ntax = false, found_nchar = false,
+       found_equal = false;
   char x = '=';
   int lnum, eulnum;
   // getline line by line
-  for(lnum=0;getline(matrixfile,snall);lnum++){
-  str_a = to_lower(snall);
-  str_b = add_space(x,str_a);
-  istringstream istr(str_b);
-        // convert to words
-	while(istr>> stri){
-	if(stri=="dimensions"){
-		found = true;
-	} else if(stri=="ntax"){
-		found_ntax = true;
-	} else if(stri=="nchar"){
-		found_nchar = true;
-	} else if(stri=="="){
-		found_equal = true;
-	} else if (found_ntax&&found_equal){
-		if(stri.back()==';'){
-			stri.pop_back();
-			found = false;
-		}
-		ntax = stoi(stri);
-		found_equal = false;
-		found_ntax = false;	
-	} else if (found_nchar&&found_equal){
-		if(stri.back()==';'){
-			stri.pop_back();
-			found = false;
-		} 
-		nchar = stoi(stri);
-		found_equal = false;
-		found_nchar = false;
-	} else if (stri=="matrix"){
-		eulnum = lnum+1;
-	} 
+  for (lnum = 0; getline(matrixfile, snall); lnum++) {
+    str_a = to_lower(snall);
+    str_b = add_space(x, str_a);
+    istringstream istr(str_b);
+    // convert to words
+    while (istr >> stri) {
+      if (stri == "dimensions") {
+        found = true;
+      } else if (stri == "ntax") {
+        found_ntax = true;
+      } else if (stri == "nchar") {
+        found_nchar = true;
+      } else if (stri == "=") {
+        found_equal = true;
+      } else if (found_ntax && found_equal) {
+        if (stri.back() == ';') {
+          stri.pop_back();
+          found = false;
+        }
+        ntax = stoi(stri);
+        found_equal = false;
+        found_ntax = false;
+      } else if (found_nchar && found_equal) {
+        if (stri.back() == ';') {
+          stri.pop_back();
+          found = false;
+        }
+        nchar = stoi(stri);
+        found_equal = false;
+        found_nchar = false;
+      } else if (stri == "matrix") {
+        eulnum = lnum + 1;
+      }
     }
   }
   // go back
   matrixfile.clear();
   matrixfile.seekg(0);
   // create class
-  Sample sam(ntax,nchar);
+  Sample sam(ntax, nchar);
   // some temp, z is line number, l is the string arrary number
-  int z=0; int l=0;
+  int z = 0;
+  int l = 0;
   // read line by line
-  while(getline(matrixfile,snall)){
-  // convert to word
-  istringstream istr(snall);
-  // limit the read line number
-  if(z>(eulnum-1)&&z<(eulnum+sam.ntax)){
-    istr >> sam.taxas[l];
-    istr >> sam.chars[l];
-    l++;
-  }
-  z++;
+  while (getline(matrixfile, snall)) {
+    // convert to word
+    istringstream istr(snall);
+    // limit the read line number
+    if (z > (eulnum - 1) && z < (eulnum + sam.ntax)) {
+      istr >> sam.taxas[l];
+      istr >> sam.chars[l];
+      l++;
+    }
+    z++;
   }
   return sam;
 }
-string add_space (char x, string str_old) {
-	int i;
-	string str_new;
-	for (i=0; i<str_old.length(); i++) {
-		if (str_old[i] != x) {
-			str_new=str_new+str_old[i];
-		} else {
-			str_new=str_new+" "+str_old[i]+" ";
-		}
-	}
-	return str_new;
+string add_space(char x, string str_old) {
+  int i;
+  string str_new;
+  for (i = 0; i < str_old.length(); i++) {
+    if (str_old[i] != x) {
+      str_new = str_new + str_old[i];
+    } else {
+      str_new = str_new + " " + str_old[i] + " ";
+    }
+  }
+  return str_new;
 }
 
-string to_lower(string stri){
-  transform(stri.begin(),stri.end(),stri.begin(),::tolower);
+string to_lower(string stri) {
+  transform(stri.begin(), stri.end(), stri.begin(), ::tolower);
   return stri;
 }
 
-void writeFas(class Sample sam, char* otn){
+void writeFas(class Sample sam, char* otn) {
   ofstream matrixfile(otn);
-      for(int i=0;i<sam.ntax;i++){
-        matrixfile << ">" << sam.taxas[i] << endl;
-        matrixfile << sam.chars[i] << endl;
-      }
+  for (int i = 0; i < sam.ntax; i++) {
+    matrixfile << ">" << sam.taxas[i] << endl;
+    matrixfile << sam.chars[i] << endl;
+  }
   matrixfile.close();
 }
 
-void writePhy(class Sample sam, char* otn){
+void writePhy(class Sample sam, char* otn) {
   ofstream matrixfile(otn);
-      matrixfile << sam.ntax << " " << sam.nchar << endl;
-      for(int i=0;i<sam.ntax;i++){
-        matrixfile << sam.taxas[i] << "\t" << sam.chars[i]  << endl;
-      }
+  matrixfile << sam.ntax << " " << sam.nchar << endl;
+  for (int i = 0; i < sam.ntax; i++) {
+    matrixfile << sam.taxas[i] << "\t" << sam.chars[i] << endl;
+  }
   matrixfile.close();
 }
 
-void writeNex(class Sample sam, char* otn){
+void writeNex(class Sample sam, char* otn) {
   ofstream matrixfile(otn);
   string datatype;
   datatype = checktype(sam.chars[0]);
-      matrixfile << "#NEXUS" << endl; 
-      matrixfile << "Begin data;" << endl << "\tDimensions nchar=" << sam.nchar << " ntax=" << sam.ntax << ";" << endl << "\tFormat datatype=" << datatype << " missing=? gap=-;" << endl << "\tMatrix" << endl;
-      for(int i2=0;i2<sam.ntax;i2++){
-        matrixfile << "\t\t" << sam.taxas[i2] << "\t" << sam.chars[i2] << endl;
-      }
-      matrixfile << "\t;" << endl << "End;" << endl;
+  matrixfile << "#NEXUS" << endl;
+  matrixfile << "Begin data;" << endl
+             << "\tDimensions nchar=" << sam.nchar << " ntax=" << sam.ntax
+             << ";" << endl
+             << "\tFormat datatype=" << datatype << " missing=? gap=-;" << endl
+             << "\tMatrix" << endl;
+  for (int i2 = 0; i2 < sam.ntax; i2++) {
+    matrixfile << "\t\t" << sam.taxas[i2] << "\t" << sam.chars[i2] << endl;
+  }
+  matrixfile << "\t;" << endl << "End;" << endl;
   matrixfile.close();
 }
 
-string checktype(string str){
+string checktype(string str) {
   // some var
   float a, c, t, g, zero, one, two, dna, standard;
-  char ca='a', cc='c', ct='t', cg='g', czero='0', cone='1', ctwo='2';
+  char ca = 'a', cc = 'c', ct = 't', cg = 'g', czero = '0', cone = '1',
+       ctwo = '2';
   string datatype;
   // count fre
   a = countfre(str, ca);
@@ -292,131 +301,134 @@ string checktype(string str){
   one = countfre(str, cone);
   two = countfre(str, ctwo);
   // summary dna or morphology
-  dna = a+c+t+g;
-  standard = zero+one+two;
+  dna = a + c + t + g;
+  standard = zero + one + two;
   // use percentage to test
-  if((dna/str.length())>0.7){
-      datatype = "dna"; 
-  } else if ((standard/str.length())>0.7){
-      datatype = "standard";
+  if ((dna / str.length()) > 0.7) {
+    datatype = "dna";
+  } else if ((standard / str.length()) > 0.7) {
+    datatype = "standard";
   } else {
-      datatype = "protein";
+    datatype = "protein";
   }
   return datatype;
 }
 
-int countfre(string str, char c){
+int countfre(string str, char c) {
   int num;
   str = to_lower(str);
-  num = count(str.begin(),str.end(),c); 
-  return num; 
+  num = count(str.begin(), str.end(), c);
+  return num;
 }
 
-void writeTnt(class Sample sam, char* otn){
+void writeTnt(class Sample sam, char* otn) {
   ofstream matrixfile(otn);
-      matrixfile << "xread" << endl << "\' \'" << endl;
-      matrixfile << sam.nchar << " " << sam.ntax << endl;
-      for(int i=0;i<sam.ntax;i++){
-        matrixfile << sam.taxas[i] << "\t" << sam.chars[i]  << endl;
-      }
-      matrixfile << "proc / ;" << endl;
+  matrixfile << "xread" << endl << "\' \'" << endl;
+  matrixfile << sam.nchar << " " << sam.ntax << endl;
+  for (int i = 0; i < sam.ntax; i++) {
+    matrixfile << sam.taxas[i] << "\t" << sam.chars[i] << endl;
+  }
+  matrixfile << "proc / ;" << endl;
   matrixfile.close();
 }
 
-
-Basic_arg procargs (int nargs, char ** arg, char* itn, char* otn){
-  int i, sta = 0, intype=0, outype=0;
+Basic_arg procargs(int nargs, char** arg, char* itn, char* otn) {
+  int i, sta = 0, intype = 0, outype = 0;
   string para, inputfile, outputfile;
-  //no arg, show help
-  if (nargs==1){
+  // no arg, show help
+  if (nargs == 1) {
     show_help(0);
     exit(0);
-    sta=2;
+    sta = 2;
   }
-  //recognize arg
-  for (i=1;i<nargs;i++){
-    //to string
-    string para (arg[i]);
-    if ( para =="-h"| para=="--help" ) {
-	    show_help(1);
-	    sta=2;
-    }   
-    else if ( para =="-i"| para=="--input"){
-    	i++;
-	itn=arg[i];
-        string inputfile (arg[i]);
-        intype = checkextension(inputfile);
-	sta++;	
-    }
-    else if ( para =="-o"| para=="--output"){
-        i++;
-	otn=arg[i];
-        string outputfile (arg[i]);
-        outype = checkextension(outputfile);
-	sta++;	
+  // recognize arg
+  for (i = 1; i < nargs; i++) {
+    // to string
+    string para(arg[i]);
+    if (para == "-h" | para == "--help") {
+      show_help(1);
+      sta = 2;
+    } else if (para == "-i" | para == "--input") {
+      i++;
+      itn = arg[i];
+      string inputfile(arg[i]);
+      intype = checkextension(inputfile);
+      sta++;
+    } else if (para == "-o" | para == "--output") {
+      i++;
+      otn = arg[i];
+      string outputfile(arg[i]);
+      outype = checkextension(outputfile);
+      sta++;
     } else {
       cout << "MiMi\tUnknown arguments, please use -h to check" << endl;
       exit(0);
     }
   }
-    if(sta!=2){ 
-	cout << "MiMi\tInput and Output can't be empty" << endl;
-	exit(0);
+  if (sta != 2) {
+    cout << "MiMi\tInput and Output can't be empty" << endl;
+    exit(0);
   }
-   Basic_arg arguvar(intype,outype,itn,otn);
-   return arguvar;
+  Basic_arg arguvar(intype, outype, itn, otn);
+  return arguvar;
 }
 
-int checkextension(string str){
-	int loc, type;
-	string extension;
-	loc = str.rfind('.');
-	if(loc){
-	  extension = str.substr(loc+1);
-	} else {
-	  cout << "MiMi\tPlease sepecifc the extension name" << endl;
-	  exit(0);
-	}
-	extension = to_lower(extension);
-	if(extension=="fas"|extension=="fasta"){
-		type = 1;
-	} else if (extension=="nex"|extension=="nexus"){
-		type = 2;
-	} else if (extension=="phy"|extension=="phylip"){
-		type = 3;
-	} else if (extension=="tnt"|extension=="ss"){
-		type = 4;
-	} else {
-		cout << "MiMi\tUnknown format" << endl;
-		exit(0);
-	}	
-	return type;
-}
-
-void show_help (int help_num){
-
-
-
-  if (help_num == 0){
-    cout  << "MiMi, GPL, Guoyi Zhang, 2023.\nPlease use -h to see more help" << endl;
+int checkextension(string str) {
+  int loc, type;
+  string extension;
+  loc = str.rfind('.');
+  if (loc) {
+    extension = str.substr(loc + 1);
   } else {
-    cout << "\n  ／l、    \t.  . .  .\n（ﾟ､ ｡ ７    \t|\\/|*|\\/|*\n  l  ~ヽ    \t|  |||  ||\n  じしf_,)ノ\t|  |||  ||\n" << endl;
-    cout << "Morphology into Molecules into\n" << "GPL\tGuoyi\tZhang,\t2023\n" << endl;
-    cout << "-h\t--help;\n-i\t--input\t\t${filename};\n-o\t--output\t${filename};\n" << endl;
-    cout << "Accepted format:\nfas\tfasta;\nnex\tnexus\nphy\tphylip\ntnt\tss" << endl;
+    cout << "MiMi\tPlease sepecifc the extension name" << endl;
+    exit(0);
+  }
+  extension = to_lower(extension);
+  if (extension == "fas" | extension == "fasta") {
+    type = 1;
+  } else if (extension == "nex" | extension == "nexus") {
+    type = 2;
+  } else if (extension == "phy" | extension == "phylip") {
+    type = 3;
+  } else if (extension == "tnt" | extension == "ss") {
+    type = 4;
+  } else {
+    cout << "MiMi\tUnknown format" << endl;
+    exit(0);
+  }
+  return type;
+}
+
+void show_help(int help_num) {
+  if (help_num == 0) {
+    cout << "MiMi, GPL, Guoyi Zhang, 2023.\nPlease use -h to see more help"
+         << endl;
+  } else {
+    cout << "\n  ／l、    \t.  . .  .\n（ﾟ､ ｡ ７    \t|\\/|*|\\/|*\n  l  ~ヽ   "
+            " \t|  |||  ||\n  じしf_,)ノ\t|  |||  ||\n"
+         << endl;
+    cout << "Morphology into Molecules into\n"
+         << "GPL;\tGuoyi Zhang;\t2023\n"
+         << endl;
+    cout << "-h\t--help;\n-i\t--input\t\t${filename};\n-o\t--output\t${"
+            "filename};\n"
+         << endl;
+    cout
+        << "Accepted formats:\nfas\tfasta;\nnex\tnexus;\nphy\tphylip;\ntnt\tss;"
+        << endl;
   }
 }
 
-Sample read_input (char* itn, int intype){
+Sample read_input(char* itn, int intype) {
   int ntax, nchar;
-  Sample sam(ntax,nchar);
+  Sample sam(ntax, nchar);
   ifstream matrixfile;
   matrixfile.open(itn);
-  if (matrixfile.is_open()){
-  if (intype==1) sam = readFas(itn);
-  if (intype==2) sam = readNex(itn);
-  if (intype==3) sam = readPhy(itn);
-  if (intype==4) sam = readTnt(itn);
+  if (matrixfile.is_open()) {
+    if (intype == 1) sam = readFas(itn);
+    if (intype == 2) sam = readNex(itn);
+    if (intype == 3) sam = readPhy(itn);
+    if (intype == 4) sam = readTnt(itn);
   } else {
     cout << "MiMi\tInput file can't be open" << endl;
     exit(0);
@@ -424,48 +436,47 @@ Sample read_input (char* itn, int intype){
   return sam;
 }
 
-void write_output (class Sample sam, char* otn, int outype){
+void write_output(class Sample sam, char* otn, int outype) {
   ofstream matrixfile(otn);
   if (matrixfile.is_open()) {
-  if (outype==1) writeFas(sam,otn);
-  if (outype==2) writeNex(sam,otn);
-  if (outype==3) writePhy(sam,otn);
-  if (outype==4) writeTnt(sam,otn);
+    if (outype == 1) writeFas(sam, otn);
+    if (outype == 2) writeNex(sam, otn);
+    if (outype == 3) writePhy(sam, otn);
+    if (outype == 4) writeTnt(sam, otn);
   } else {
     cout << "MiMi\tOutput file can't be open" << endl;
     exit(0);
   }
 }
 
-bool checkalign(class Sample sam){
-  int a=0, b=0, x=0;
+bool checkalign(class Sample sam) {
+  int a = 0, b = 0, x = 0;
   a = sam.nchar;
   bool aligned = true;
-  for(int i=0;i<sam.ntax;i++){
-  	b=sam.chars[i].length();
-	if(a==b){
-		x++;
-	}
+  for (int i = 0; i < sam.ntax; i++) {
+    b = sam.chars[i].length();
+    if (a == b) {
+      x++;
+    }
   }
-  if (x!=sam.ntax){
-      aligned = false;
+  if (x != sam.ntax) {
+    aligned = false;
   }
   return aligned;
 }
 
-
-int main(int argc, char **argv){
+int main(int argc, char** argv) {
   char *itn, *otn;
-  Basic_arg arguvar = procargs (argc, argv, itn, otn);
-  if(arguvar.intype!=0&&arguvar.outype!=0){
-  Sample sam = read_input(arguvar.itn,arguvar.intype);
-  cout << "MiMi:\tInput\tfinished" << endl;
-  if(!checkalign(sam)){
-    cout << "MiMi:\tInput file should be aligned" << endl;
-    exit(0);
-  }
-  write_output(sam,arguvar.otn,arguvar.outype);
-  cout << "MiMi:\tOutput\tfinished" << endl;
+  Basic_arg arguvar = procargs(argc, argv, itn, otn);
+  if (arguvar.intype != 0 && arguvar.outype != 0) {
+    Sample sam = read_input(arguvar.itn, arguvar.intype);
+    cout << "MiMi:\tInput\tfinished" << endl;
+    if (!checkalign(sam)) {
+      cout << "MiMi:\tInput file should be aligned" << endl;
+      exit(0);
+    }
+    write_output(sam, arguvar.otn, arguvar.outype);
+    cout << "MiMi:\tOutput\tfinished" << endl;
   }
   return 0;
 }