text: 
  #include <iostream>
  #include <fstream>
  #include <vector>
  #include <string>
  #include <cstring>
  #include <getopt.h>
  #include <map>
  
  using namespace std;
  
  #include "string_node_object.h"
  #include "utils.h"
  #include "sequence.h"
  #include "seq_reader.h"
  #include "tree_reader.h"
  #include "tree.h"
  #include "cont_models.h"
  #include "optimize_cont_models_nlopt.h"
  #include "log.h"
  
  void print_help() {
      cout << "Continuous character rate estimation with Brownian and OU." << endl;
      cout << "This will take fasta, phylip (and soon nexus) inputs." << endl;
      cout << "Can read from stdin or file." << endl;
      cout << endl;
      cout << "Usage: pxcontrates [OPTION]... " << endl;
      cout << endl;
      cout << " -c, --charf=FILE     input character file, stdin otherwise" << endl;
      cout << " -t, --treef=FILE     input tree file, stdin otherwise" << endl;
      cout << " -a, --analysis=NUM   analysis type (0=anc[DEFAULT], 1=ratetest)" << endl;
      cout << " -o, --outf=FILE      output sequence file, stout otherwise" << endl;
      cout << " -h, --help           display this help and exit" << endl;
      cout << " -V, --version        display version and exit" << endl;
      cout << endl;
      cout << "Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>" << endl;
      cout << "phyx home page: <https://github.com/FePhyFoFum/phyx>" << endl;
  }
  
  string versionline("pxcontrates 0.1\nCopyright (C) 2013 FePhyFoFum\nLicense GPLv3\nwritten by Joseph W. Brown, Stephen A. Smith (blackrim)");
  
  static struct option const long_options[] =
  {
      {"char", required_argument, NULL, 'c'},
      {"tree", required_argument, NULL, 't'},
      {"outf", required_argument, NULL, 'o'},
      {"analysis", required_argument, NULL, 'a'},
      {"help", no_argument, NULL, 'h'},
      {"version", no_argument, NULL, 'V'},
      {NULL, 0, NULL, 0}
  };
  
  int main(int argc, char * argv[]) {
      
      log_call(argc, argv);
      
      bool cfileset = false;
      bool tfileset = false;
      bool outfileset = false;
      
      char * treef = NULL;
      char * charf = NULL;
      char * outf = NULL;
      int analysis = 0;
      while (1) {
          int oi = -1;
          int c = getopt_long(argc, argv, "c:t:o:a:hV", long_options, &oi);
          if (c == -1) {
              break;
          }
          switch(c) {
              case 'c':
                  cfileset = true;
                  charf = strdup(optarg);
                  check_file_exists(charf);
                  break;
              case 't':
                  tfileset = true;
                  treef = strdup(optarg);
                  check_file_exists(treef);
                  break;
              case 'o':
                  outfileset = true;
                  outf = strdup(optarg);
                  break;
              case 'a':
                  if (optarg[0] == '1') {
                      analysis = 1;
                  }
                  break;
              case 'h':
                  print_help();
                  exit(0);
              case 'V':
                  cout << versionline << endl;
                  exit(0);
              default:
                  print_error(argv[0], (char)c);
                  exit(0);
          }
      }
  
      istream * pios = NULL;
      istream * poos = NULL;
      ifstream * cfstr = NULL;
      ifstream * tfstr = NULL;
  
      ostream * poouts = NULL;
      ofstream * ofstr = NULL;
      
  
      if (tfileset == true) {
          tfstr = new ifstream(treef);
          poos = tfstr;
      } else {
          poos = &cin;
      }
  
      if (cfileset == true) {
          cfstr = new ifstream(charf);
          pios = cfstr;
      } else {
          cout << "you have to set a character file. Only a tree file can be read in through the stream;" << endl;
      }
  
      //out file
      //
      if (outfileset == true) {
          ofstr = new ofstream(outf);
          poouts = ofstr;
      } else {
          poouts = &cout;
      }
      //
  
      string retstring;
      int ft = test_char_filetype_stream(*pios, retstring);
      if (ft != 1 && ft != 2) {
          cout << "only fasta and phylip (with spaces) supported so far" << endl;
          exit(0);
      }
      Sequence seq;
      vector <Sequence> seqs;
      map <string, int> seq_map;
      int y = 0;
      int nchars = 0 ;
      while (read_next_seq_char_from_stream(*pios, ft, retstring, seq)) {
          seqs.push_back(seq);
          nchars = seq.get_num_cont_char();
          seq_map[seq.get_id()] = y;
          seq.clear_cont_char();
          y++;
      }
      
      if (ft == 2) {
          seqs.push_back(seq);
          seq_map[seq.get_id()] = y;
          seq.clear_cont_char();
      }
      //read trees
      TreeReader tr;
      vector<Tree *> trees;
      while (getline(*poos,retstring)) {
          trees.push_back(tr.readTree(retstring));
      }
      
      //conduct analyses for each character
      for (int c=0; c < nchars; c++) {
          cerr << "character: " << c << endl;
          if (analysis == 0) {
             // cout << "Input tree: " << getNewickString(trees[0]) << ";" << endl;
              if (c == 0) {
                  (*poouts) << "#nexus" << endl << "begin trees;" << endl;
              }
              for (unsigned int x = 0; x < trees.size(); x++){
                  for (int i=0; i < trees[x]->getExternalNodeCount(); i++) {
                      vector<Superdouble> tv (1);
                      tv[0] = seqs[seq_map[trees[x]->getExternalNode(i)->getName()]].get_cont_char(c);
                      trees[x]->getExternalNode(i)->assocDoubleVector("val",tv);
                  }
                  for (int i=0; i < trees[x]->getInternalNodeCount(); i++) {
                      vector<Superdouble> tv (1);
                      tv[0] = 0;
                      trees[x]->getInternalNode(i)->assocDoubleVector("val",tv);
                  }
                  calc_square_change_anc_states(trees[x],0); // second character dies here
                  for (int i=0; i < trees[x]->getInternalNodeCount(); i++) {
                      double tv = (*trees[x]->getInternalNode(i)->getDoubleVector("val"))[0];
                      trees[x]->getInternalNode(i)->deleteDoubleVector("val");
                      std::ostringstream s;
                      s.precision(9);
                      s << fixed << tv;
                      StringNodeObject nob(s.str());
                      trees[x]->getInternalNode(i)->assocObject("value",nob);
                      //trees[x]->getInternalNode(i)->setName(s.str());
                  }
                  for (int i=0; i < trees[x]->getExternalNodeCount(); i++) {
                      double tv = (*trees[x]->getExternalNode(i)->getDoubleVector("val"))[0];
                      trees[x]->getExternalNode(i)->deleteDoubleVector("val");
                      std::ostringstream s;
                      s.precision(9);
                      s << fixed << tv;
                      StringNodeObject nob(s.str());
                      trees[x]->getExternalNode(i)->assocObject("value",nob);
                      //s << fixed << trees[x]->getExternalNode(i)->getName() << "[&value=" << tv << "]";
                      //trees[x]->getExternalNode(i)->setName(s.str());
                  }
                  (*poouts) << "tree tree" << c << " = ";
                  (*poouts) << getNewickString(trees[x],"value") << endl;
              }
              if (c == (nchars - 1)) {
                  (*poouts) << "end;\n" << endl;
              }
              // remove annotations
              remove_annotations(trees[0]);
              
          } else if (analysis == 1) {
              mat vcv;
              int t_ind = 0; // TODO: do this over trees
              int c_ind = c;
              calc_vcv(trees[t_ind],vcv);
              int n = trees[t_ind]->getExternalNodeCount();
              rowvec x = rowvec(n);
              for (int i=0; i < n; i++) {
                  x(i) = seqs[seq_map[trees[t_ind]->getExternalNode(i)->getName()]].get_cont_char(c_ind);
              }
              vector<double> res = optimize_single_rate_bm_nlopt(x, vcv, true);
              double aic = (2*2)-(2*(-res[2]));
              double aicc = aic + ((2*2*(2+1))/(n-2-1));
              cout << c << " BM " << " state: " << res[0] <<  " rate: " << res[1]
                  << " like: " << -res[2] << " aic: " << aic << " aicc: " << aicc <<  endl;
  
              vector<double> res2 = optimize_single_rate_bm_ou_nlopt(x, vcv);
              aic = (2*3)-(2*(-res2[3]));
              aicc = aic + ((2*3*(3+1))/(n-3-1));
              cout << c << " OU " << " state: " << res2[0] <<  " rate: "
                  << res2[1] << " alpha: " << res2[2] <<  " like: " << -res2[3]
                  << " aic: " << aic << " aicc: " << aicc << endl;
          }
      }
  
      if (cfileset) {
          cfstr->close();
          delete pios;
      }
      if (tfileset) {
          tfstr->close();
          delete poos;
      }
      if (outfileset) {
          ofstr->close();
          delete poouts;
      }
      return EXIT_SUCCESS;
  }
  