diff --git a/misc/Jamfile b/misc/Jamfile
index 1e5929570..81fcb7043 100644
--- a/misc/Jamfile
+++ b/misc/Jamfile
@@ -46,4 +46,4 @@ $(TOP)//boost_iostreams
 $(TOP)//boost_program_options 
 ; 
 
-alias programs : 1-1-Extraction TMining generateSequences processPhraseTable processLexicalTable queryPhraseTable queryLexicalTable programsMin programsProbing merge-sortedprune PhraseTable  ;
+alias programs : 1-1-Extraction TMining generateSequences processPhraseTable processLexicalTable queryPhraseTable queryLexicalTable programsMin programsProbing merge-sorted prunePhraseTable  ;
diff --git a/misc/prunePhraseTable.cpp b/misc/prunePhraseTable.cpp
index 745b9cb45..a6158a4ab 100644
--- a/misc/prunePhraseTable.cpp
+++ b/misc/prunePhraseTable.cpp
@@ -34,7 +34,9 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #include <boost/program_options.hpp>
 #include <boost/scoped_ptr.hpp>
 
+#include "moses/InputPath.h"
 #include "moses/Parameter.h"
+#include "moses/TranslationModel/PhraseDictionary.h"
 #include "moses/StaticData.h"
 
 #include "util/file_piece.hh"
@@ -55,7 +57,45 @@ static void usage(const po::options_description& desc, char** argv) {
 }
 
 //Find top n translations of source, and send them to output
-static void outputTopN(const StringPiece& sourcePhrase, const StaticData& staticData, ostream& out) {
+static void outputTopN(const StringPiece& sourcePhraseString, PhraseDictionary* phraseTable, const std::vector<FactorType> &input,  ostream& out) {
+  //get list of target phrases
+  Phrase sourcePhrase;
+  sourcePhrase.CreateFromString(Input,input,sourcePhraseString,NULL);
+  InputPath inputPath(sourcePhrase, NonTerminalSet(), WordsRange(0,sourcePhrase.GetSize()-1),NULL,NULL);
+  InputPathList inputPaths;
+  inputPaths.push_back(&inputPath);
+  phraseTable->GetTargetPhraseCollectionBatch(inputPaths);
+  
+
+  //EvaluateInIsolation ??
+  const TargetPhraseCollection* targetPhrases = inputPath.GetTargetPhrases(*phraseTable);
+
+  //sort by total score and prune
+  // - Already done?
+
+
+  //print phrases
+  const std::vector<FactorType>& output = StaticData::Instance().GetOutputFactorOrder();
+  if (targetPhrases) {
+    for (TargetPhraseCollection::const_iterator i = targetPhrases->begin(); i != targetPhrases->end(); ++i) {
+      const TargetPhrase* targetPhrase = *i;
+      out << sourcePhrase.GetStringRep(input);
+      out << " ||| ";
+      out << targetPhrase->GetStringRep(output);
+      out << " ||| ";
+      const ScoreComponentCollection scores = targetPhrase->GetScoreBreakdown();
+      vector<float> phraseScores = scores.GetScoresForProducer(phraseTable);
+      for (size_t j = 0; j < phraseScores.size(); ++j) {
+        out << exp(phraseScores[j]) << " ";
+      }
+      out << "||| ";
+      const AlignmentInfo& align = targetPhrase->GetAlignTerm();
+      for (AlignmentInfo::const_iterator j = align.begin(); j != align.end(); ++j) {
+        out << j->first << "-" << j->second << " ";
+      }
+      out << endl;
+    }
+  }
 
 }
 
@@ -63,7 +103,6 @@ int main(int argc, char** argv)
 {
   bool help;
   string input_file;
-  string output_file;
   string config_file;
 
 
@@ -71,15 +110,15 @@ int main(int argc, char** argv)
   desc.add_options()
   ("help,h", po::value(&help)->zero_tokens()->default_value(false), "Print this help message and exit")
   ("input-file,i", po::value<string>(&input_file), "Input file")
-  ("output-file,o", po::value<string>(&output_file), "Output file")
   ("config-file,f", po::value<string>(&config_file), "Config file")
   ;
 
   po::options_description cmdline_options;
   cmdline_options.add(desc);
   po::variables_map vm;
-  po::store(po::command_line_parser(argc,argv).
-            options(cmdline_options).run(), vm);
+  po::parsed_options parsed = po::command_line_parser(argc,argv).
+            options(cmdline_options).allow_unregistered().run();
+  po::store(parsed, vm);
   po::notify(vm);
   if (help) {
     usage(desc, argv);
@@ -90,11 +129,6 @@ int main(int argc, char** argv)
     usage(desc, argv);
     exit(1);
   }
-  if (output_file.empty()) {
-    cerr << "ERROR: Please specify an output file" << endl << endl;
-    usage(desc, argv);
-    exit(1);
-  }
   if (config_file.empty()) {
     cerr << "ERROR: Please specify a config file" << endl << endl;
     usage(desc, argv);
@@ -105,6 +139,19 @@ int main(int argc, char** argv)
   mosesargs.push_back(argv[0]);
   mosesargs.push_back("-f");
   mosesargs.push_back(config_file);
+  for (size_t i = 0; i < parsed.options.size(); ++i) {
+    if (parsed.options[i].position_key == -1 && !parsed.options[i].unregistered) continue;
+    const string& key = parsed.options[i].string_key;
+    if (!key.empty()) {
+      mosesargs.push_back(key);
+    }
+    for (size_t j = 0; j < parsed.options[i].value.size(); ++j) {
+      const string& value = parsed.options[i].value[j];
+      if (!value.empty()) {
+        mosesargs.push_back(value);
+      }
+    }
+  }
 
   boost::scoped_ptr<Parameter> params(new Parameter());  
   char** mosesargv = new char*[mosesargs.size()];
@@ -122,11 +169,27 @@ int main(int argc, char** argv)
     exit(1);
   }
 
+  const StaticData &staticData = StaticData::Instance();
+  const std::vector<FactorType> & input = staticData.GetInputFactorOrder();
+
+  //Find the phrase table to evaluate with
+  PhraseDictionary* phraseTable = NULL;
+  const vector<FeatureFunction*>& ffs = FeatureFunction::GetFeatureFunctions();
+  for (size_t i = 0; i < ffs.size(); ++i) {
+    PhraseDictionary* maybePhraseTable = dynamic_cast< PhraseDictionary*>(ffs[i]);
+    if (maybePhraseTable) {
+      UTIL_THROW_IF(phraseTable,util::Exception,"Can only score translations with one phrase table");
+      phraseTable = maybePhraseTable;
+    }
+  }
+  UTIL_THROW_IF(!phraseTable,util::Exception,"Unable to find scoring phrase table");
+
+  Sentence sentence;
+  phraseTable->InitializeForInput(sentence);
 
   //
   //Load and prune the phrase table. This is taken (with mods) from moses/TranslationModel/RuleTable/LoaderStandard.cpp
   //
-  const StaticData &staticData = StaticData::Instance();
 
   string lineOrig;
 
@@ -152,9 +215,11 @@ int main(int argc, char** argv)
     util::TokenIter<util::MultiCharacter> pipes(line, "|||");
     StringPiece sourcePhraseString(*pipes);
     if (sourcePhraseString != previous) {
-      outputTopN(previous, staticData, cout);
+      outputTopN(previous, phraseTable, input, cout);
+      previous = sourcePhraseString;
     }
   }
+  outputTopN(previous, phraseTable, input, cout);