diff --git a/LICENSE b/LICENSE
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--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,30 @@
+Copyright (c) 2013, Florian Eggenhofer
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+
+    * Redistributions in binary form must reproduce the above
+      copyright notice, this list of conditions and the following
+      disclaimer in the documentation and/or other materials provided
+      with the distribution.
+
+    * Neither the name of Florian Eggenhofer nor the names of other
+      contributors may be used to endorse or promote products derived
+      from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/Setup.hs b/Setup.hs
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--- /dev/null
+++ b/Setup.hs
@@ -0,0 +1,2 @@
+import Distribution.Simple
+main = defaultMain
diff --git a/memexml.cabal b/memexml.cabal
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--- /dev/null
+++ b/memexml.cabal
@@ -0,0 +1,64 @@
+-- Initial memexml.cabal generated by cabal init.  For further 
+-- documentation, see http://haskell.org/cabal/users-guide/
+
+-- The name of the package.
+name:                memexml
+
+-- The package version.  See the Haskell package versioning policy (PVP) 
+-- for standards guiding when and how versions should be incremented.
+-- http://www.haskell.org/haskellwiki/Package_versioning_policy
+-- PVP summary:      +-+------- breaking API changes
+--                   | | +----- non-breaking API additions
+--                   | | | +--- code changes with no API change
+version:             0.0.1
+
+-- A short (one-line) description of the package.
+synopsis:            Library for reading Meme XML output
+
+-- A longer description of the package.
+description:         Parse Multiple EM for Motif Elicitation (MEME) XML output.
+		     XML parsing is done with the HXT libary.
+		     .
+	   	     For more information on MEME consult: <http://meme.nbcr.net/meme/>
+                     .
+		     The memexml git repository can be found at: <https://github.com/eggzilla/memexml>
+
+-- The license under which the package is released.
+license:             BSD3
+
+-- The file containing the license text.
+license-file:        LICENSE
+
+-- The package author(s).
+author:              Florian Eggenhofer
+
+-- An email address to which users can send suggestions, bug reports, and 
+-- patches.
+maintainer:          egg@tbi.univie.ac.at
+
+-- A copyright notice.
+-- copyright:           
+
+homepage:	     https://github.com/eggzilla/memexml
+
+category:            Bioinformatics
+
+build-type:          Simple
+
+-- Constraint on the version of Cabal needed to build this package.
+cabal-version:       >=1.8
+
+
+library
+  -- Modules exported by the library.
+  exposed-modules:     Bio.MemeXML, Bio.MemeData
+  
+  -- Modules included in this library but not exported.
+  -- other-modules:       
+  
+  -- Other library packages from which modules are imported.
+  build-depends:       base ==4.5.*, hxt ==9.3.*, memexml ==0.1.*
+  
+  -- Directories containing source files.
+  hs-source-dirs:      src
+  
diff --git a/src/Bio/MemeData.hs b/src/Bio/MemeData.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/MemeData.hs
@@ -0,0 +1,166 @@
+-- | This module contains a hierarchical data structure for
+--   Multiple EM for Motif Elicitation (MEME) results
+--   For more information on MEME consult: <http://meme.nbcr.net/meme/>
+
+module Bio.MemeData where
+
+-- | Document Root of Meme xml output
+data MemeResult = MemeResult 
+  { memeversion, memerelease :: String
+  , trainingset :: TrainingSet
+  , model :: Model
+  , motifs :: [Motif]
+  , scannedSiteSummary :: ScannedSiteSummary }
+  deriving (Show, Eq)
+
+-- | Training set defines the data used for the motif search
+data TrainingSet = TrainingSet
+  { trainingsetDatafile :: String
+  , trainingsetLength :: Int
+  , trainingsetAlphabet :: MemeAlphabet
+  , trainingsetAmbigs :: MemeAmbigs
+  , trainingsetSequences :: [Sequence]
+  , trainingsetLetterFrequencies :: LetterFrequencies}
+  deriving (Show, Eq)
+
+data MemeAlphabet = MemeAlphabet
+  { memeAlphabetId :: String
+  , memeAlphabetLength :: Int
+  , memeAlphabetLetters :: [MemeLetter]}
+  deriving (Show, Eq)     
+         
+data MemeLetter = MemeLetter
+  { memeLetterId :: String
+  , memeLetterSymbol :: Char}
+  deriving (Show, Eq)
+
+data MemeAmbigs = MemeAmbigs
+  { memeAmbigLetters :: [MemeLetter]}
+  deriving (Show, Eq)
+           
+data Sequence = Sequence
+  { sequenceId :: String
+  , sequenceName :: String
+  , sequenceLength :: Int
+  , sequenceWeight :: Double}
+  deriving (Show, Eq)
+
+data LetterFrequencies = LetterFrequencies
+  { letterFrequenciesAlphabetArray :: AlphabetArray}
+  deriving (Show, Eq)
+           
+-- The model describes how to training set was processed
+data Model = Model
+  { commandLine :: String
+  , host :: String
+  , modelType :: String
+  , nmotifs :: Int
+  , evalueThreshold :: String
+  , objectFunction :: String
+  , minWidth :: Int
+  , maxWidth :: Int
+  , minic :: Double
+  , wg :: Int
+  , ws :: Int
+  , endGaps :: String
+  , minSites :: Int
+  , maxSites :: Int
+  , wnSites :: Double
+  , prob :: Int
+  , spMap :: String
+  , spFuzz :: Double
+  , prior :: String
+  , beta :: Double
+  , maxiter :: Int
+  , distance :: Double
+  , numSequences :: Int
+  , numPositions :: Int
+  , seed :: Int
+  , seqfrac :: String
+  , strands :: String
+  , priorsFile :: String
+  , reasonForStopping :: String
+  , backgroundFrequencies :: BackgroundFrequencies}
+  deriving (Show, Eq)        
+
+data BackgroundFrequencies = BackgroundFrequencies
+  { source :: String
+  , backgroundFrequenciesAlphabetArray :: AlphabetArray}
+  deriving (Show, Eq)
+
+data AlphabetArray = AlphabetArray
+  { alphabetArrayValues :: [AlphabetArrayValue]}
+  deriving (Show, Eq)
+
+data AlphabetArrayValue = AlphabetArrayValue
+  { letterId :: String,
+    frequency :: Double}
+  deriving (Show, Eq)
+
+-- | The motifs are predicted by appying the model to the trainingset
+data Motif = Motif
+  { motifId :: String
+  , motifName :: String
+  , motifWidth :: Int
+  , motifSites :: Int
+  , motifIc :: Double
+  , motifRe :: Double
+  , motifLlr :: Int
+  , motifEvalue :: Double
+  , motifBayesTreshold :: Double
+  , motifElapsedTime :: Double                          
+  , motifRegularexpression :: String
+  , motifScores :: Scores
+  , motifProbabilites :: Propabilities                
+  , motifContributingsites :: [ContributingSite]}
+  deriving (Show, Eq)
+
+data Scores = Scores
+  { scoreAlphabetMatrix :: AlphabetMatrix}
+  deriving (Show, Eq)
+
+data Propabilities = Propabilities
+  { propabilitiesAlphabetMatrix :: AlphabetMatrix}
+  deriving (Show, Eq)
+
+data AlphabetMatrix = AlphabetMatrix
+  { alphabetMatrixArrays :: [AlphabetArray]}
+  deriving (Show, Eq)        
+  
+data ContributingSite = ContributingSite
+  { contributingSiteId :: String
+  , contributingSitePosition :: Int
+  , contributingSiteStrand :: String
+  , contributingSitePvalue :: Double
+  , contributingSiteLeftFlank :: String
+  , contributingSiteRightFlank :: String
+  , contributingSite :: Site}
+  deriving (Show, Eq)
+
+data Site = Site
+  { siteLetterReferences :: [LetterReference]}
+  deriving (Show, Eq)
+             
+data LetterReference = LetterReference
+  { letterReference :: String}
+  deriving (Show, Eq)
+
+-- | Scanned sites contain all sites evaluated for possible motifs 
+data ScannedSiteSummary = ScannedSiteSummary
+  { pThresh :: Double
+  , scannedSites :: [ScannedSites]}
+  deriving (Show, Eq)
+           
+data ScannedSites = ScannedSites
+  { scannedsitesSequenceId :: String              
+  , scannedSitesPvalue :: Double
+  , numSites :: Int
+  , scannedSiteArray :: [ScannedSite]}
+  deriving (Show, Eq)
+           
+data ScannedSite = ScannedSite
+  { scannedsiteMotifId :: String              
+  , strand :: String
+  , position :: Int
+  , scannedSitePvalue :: Double}
+  deriving (Show, Eq)
diff --git a/src/Bio/MemeXML.hs b/src/Bio/MemeXML.hs
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--- /dev/null
+++ b/src/Bio/MemeXML.hs
@@ -0,0 +1,344 @@
+{-# LANGUAGE Arrows #-}
+
+-- | Parse Multiple EM for Motif Elicitation (MEME) XML output.
+--   xml parsing is done with the HXT libary.
+--   For more information on MEME consult: <http://meme.nbcr.net/meme/>
+module Bio.MemeXML ( parseXML
+                   , atTag
+                   , atId
+                   , rstrip
+                   , getMemeResult
+                   , getTrainingSet
+                   , getMemeAlphabet
+                   , getLetter
+                   , getAmbigs
+                   , getLetterFrequencies
+                   , getModel
+                   , getBackgroundFrequencies
+                   , getScannedSiteSummary
+                   , getScannedSites
+                   , getScannedSite
+                   , getSequence
+                   , getMotif
+                   , getContributingSite
+                   , module Bio.MemeData) where
+
+import Bio.MemeData
+import Text.XML.HXT.Core
+import Data.Char (isSpace)    
+
+-- | Parse XML results in XML format
+parseXML :: String -> IOStateArrow s b XmlTree              
+parseXML = readDocument [ withValidate no
+                        , withRemoveWS yes  -- throw away formating WS
+                        ] 
+           
+-- | gets all subtrees with the specified tag name
+atTag :: ArrowXml a =>  String -> a XmlTree XmlTree
+atTag tag = deep (isElem >>> hasName tag)
+
+-- | gets all subtrees with the specified id attribute
+atId :: ArrowXml a =>  String -> a XmlTree XmlTree
+atId elementId = deep (isElem >>> hasAttrValue "id" (== elementId))
+
+-- | removes whitespace characters                 
+rstrip :: String -> String
+rstrip = reverse . dropWhile isSpace . reverse
+
+-- | gets the whole memexml document tree 
+getMemeResult :: ArrowXml a => a XmlTree MemeResult  
+getMemeResult = atTag "MEME" >>> 
+  proc memeResult -> do
+  memeResult_version <- getAttrValue "version" -< memeResult
+  memeResult_release <- getAttrValue "release" -< memeResult
+  memeResult_training_set  <- getTrainingSet -< memeResult
+  memeResult_model  <- getModel -< memeResult
+  memeResult_motifs  <- listA getMotif -< memeResult
+  memeResult_scanned_site_summary  <- getScannedSiteSummary -< memeResult
+  returnA -< MemeResult {
+    memeversion = memeResult_version,
+    memerelease = memeResult_release,
+    trainingset = memeResult_training_set,
+    model = memeResult_model,
+    motifs = memeResult_motifs,
+    scannedSiteSummary = memeResult_scanned_site_summary}
+  
+-- | get the Training set subtree
+getTrainingSet :: ArrowXml a => a XmlTree TrainingSet  
+getTrainingSet = atTag "training_set" >>> 
+  proc trainingSet -> do
+  trainingSet_datafile <- getAttrValue "datafile" -< trainingSet
+  trainingSet_length <- getAttrValue "length" -< trainingSet
+  trainingSet_alphabet <- getMemeAlphabet -< trainingSet
+  trainingSet_ambigs <- getAmbigs -< trainingSet
+  trainingSet_sequences <- listA getSequence -< trainingSet
+  trainingSet_letterfrequencies <- getLetterFrequencies -< trainingSet
+  returnA -< TrainingSet {
+    trainingsetDatafile = trainingSet_datafile,
+    trainingsetLength = read trainingSet_length :: Int,
+    trainingsetAlphabet = trainingSet_alphabet,
+    trainingsetAmbigs = trainingSet_ambigs,
+    trainingsetSequences = trainingSet_sequences,
+    trainingsetLetterFrequencies = trainingSet_letterfrequencies}
+
+getMemeAlphabet :: ArrowXml a => a XmlTree MemeAlphabet
+getMemeAlphabet = atTag "alphabet" >>> 
+  proc memealphabet -> do
+    alphabet_id <- getAttrValue "id" -< memealphabet
+    alphabet_length <- getAttrValue "length" -< memealphabet
+    alphabet_letters <- listA getLetter -< memealphabet
+    returnA -< MemeAlphabet {
+      memeAlphabetId = alphabet_id, 
+      memeAlphabetLength = read alphabet_length :: Int,
+      memeAlphabetLetters = alphabet_letters}
+
+getLetter :: ArrowXml a => a XmlTree MemeLetter
+getLetter = atTag "letter" >>> 
+  proc memeletter -> do
+    letter_id <- getAttrValue "id" -< memeletter
+    letter_symbol <- getAttrValue "symbol" -< memeletter
+    returnA -< MemeLetter {
+      memeLetterId = letter_id, 
+      memeLetterSymbol = read letter_symbol :: Char}
+
+getAmbigs :: ArrowXml a => a XmlTree MemeAmbigs
+getAmbigs = atTag "ambigs" >>> 
+  proc memeambigs -> do
+    ambigs_letters <- listA getLetter -< memeambigs
+    returnA -< MemeAmbigs {
+      memeAmbigLetters = ambigs_letters} 
+
+getLetterFrequencies :: ArrowXml a => a XmlTree LetterFrequencies
+getLetterFrequencies = atTag "letter_frequencies" >>> 
+  proc memeletterfrequencies -> do
+    letterfrequencies_alphabetarray <- getAlphabetArray -< memeletterfrequencies
+    returnA -< LetterFrequencies {
+      letterFrequenciesAlphabetArray = letterfrequencies_alphabetarray} 
+  
+getAlphabetArray :: ArrowXml a => a XmlTree AlphabetArray
+getAlphabetArray =  atTag "alphabet_array" >>> 
+  proc memealphabetarray -> do
+    alphabetarray_values <- listA getAlphabetArrayValues -< memealphabetarray
+    returnA -< AlphabetArray {
+      alphabetArrayValues = alphabetarray_values} 
+
+getAlphabetArrayValues :: ArrowXml a => a XmlTree AlphabetArrayValue
+getAlphabetArrayValues =  atTag "alphabet_array_value" >>> 
+  proc memealphabetarrayvalue -> do
+    alphabetarrayvalue_id <- getAttrValue "letter_id" -< memealphabetarrayvalue
+    alphabetarrayvalue_frequency <- getText <<< getChildren -< memealphabetarrayvalue
+    returnA -< AlphabetArrayValue {
+      letterId = alphabetarrayvalue_id,
+      frequency = read alphabetarrayvalue_frequency :: Double} 
+
+-- | get the model subtree    
+getModel :: ArrowXml a => a XmlTree Model
+getModel = atTag "model" >>>
+  proc mememodel -> do
+     model_command_line <- getText <<< getChildren <<< atTag "command_line" -< mememodel
+     model_host <- getText <<< getChildren <<< atTag "host" -< mememodel
+     model_type <- getText <<< getChildren <<< atTag "type" -< mememodel
+     model_nmotifs <- getText <<< getChildren <<< atTag "nmotifs" -< mememodel
+     model_evalue_threshold <- getText <<< getChildren <<< atTag "evalue_threshold" -< mememodel
+     model_object_function <- getText <<< getChildren <<< atTag "object_function" -< mememodel
+     model_min_width <- getText <<< getChildren <<< atTag "min_width" -< mememodel
+     model_max_width <- getText <<< getChildren <<< atTag "max_width" -< mememodel
+     model_minic <- getText <<< getChildren <<< atTag "minic" -< mememodel
+     model_wg <- getText <<< getChildren <<< atTag "wg" -< mememodel
+     model_ws <- getText <<< getChildren <<< atTag "ws"-< mememodel
+     model_endgaps <- getText <<< getChildren <<< atTag "endgaps" -< mememodel
+     model_minsites <- getText <<< getChildren <<< atTag "minsites" -< mememodel
+     model_maxsites <- getText <<< getChildren <<< atTag "maxsites" -< mememodel
+     model_wnsites <- getText <<< getChildren <<< atTag "wnsites" -< mememodel
+     model_prob <- getText <<< getChildren <<< atTag "prob" -< mememodel
+     model_spmap <- getText <<< getChildren <<< atTag "spmap" -< mememodel
+     model_spfuzz <- getText <<< getChildren <<< atTag "spfuzz" -< mememodel
+     model_prior <- getText <<< getChildren <<< atTag "prior"-< mememodel
+     model_beta <- getText <<< getChildren <<< atTag "beta" -< mememodel
+     model_maxiter <- getText <<< getChildren <<< atTag "maxiter" -< mememodel
+     model_distance <- getText <<< getChildren <<< atTag "distance" -< mememodel
+     model_num_sequences <- getText <<< getChildren <<< atTag "num_sequences" -< mememodel
+     model_num_positions <- getText <<< getChildren <<< atTag "num_positions" -< mememodel
+     model_seed <- getText <<< getChildren <<< atTag "seed" -< mememodel
+     model_seqfrac <- getText <<< getChildren <<< atTag "seqfrac" -< mememodel
+     model_strands <- getText <<< getChildren <<< atTag "strands" -< mememodel
+     model_priors_file <- getText <<< getChildren <<< atTag "priors_file" -< mememodel
+     model_reason_for_stopping <- getText <<< getChildren <<< atTag "reason_for_stopping"-< mememodel
+     model_background_frequencies <- getBackgroundFrequencies -< mememodel
+     returnA -< Model {
+        commandLine = model_command_line,
+        host = model_host,
+        modelType = model_type,
+        nmotifs = read model_nmotifs :: Int,
+        evalueThreshold = model_evalue_threshold,
+        objectFunction = model_object_function,
+        minWidth = read model_min_width :: Int,
+        maxWidth = read model_max_width :: Int,
+        minic = read model_minic :: Double,
+        wg = read model_wg :: Int,
+        ws = read model_ws :: Int,
+        endGaps = model_endgaps,
+        minSites = read model_minsites :: Int,
+        maxSites = read model_maxsites :: Int,
+        wnSites = read model_wnsites :: Double,
+        prob = read model_prob :: Int,
+        spMap = model_spmap,
+        spFuzz = read model_spfuzz :: Double,
+        prior = model_prior,
+        beta = read model_beta :: Double,
+        maxiter = read model_maxiter :: Int,
+        distance = read model_distance :: Double,
+        numSequences =  read model_num_sequences :: Int,
+        numPositions = read model_num_positions :: Int,
+        seed = read model_seed :: Int,
+        seqfrac = model_seqfrac,
+        strands =  model_strands,
+        priorsFile =  model_priors_file,
+        reasonForStopping =  model_reason_for_stopping,
+        backgroundFrequencies = model_background_frequencies}
+
+getBackgroundFrequencies :: ArrowXml a => a XmlTree BackgroundFrequencies
+getBackgroundFrequencies =  atTag "background_frequencies" >>> 
+  proc memebackgroundfrequencies -> do
+    backgroundfrequencies_source <- getAttrValue "source" -< memebackgroundfrequencies
+    backgroundfrequencies_alphabetarray <- getAlphabetArray -<  memebackgroundfrequencies
+    returnA -< BackgroundFrequencies {
+      source = backgroundfrequencies_source,
+      backgroundFrequenciesAlphabetArray = backgroundfrequencies_alphabetarray} 
+
+getSequence :: ArrowXml a => a XmlTree Sequence          
+getSequence = atTag "sequence" >>> 
+  proc nucleotideSequence -> do
+    nucleotide_SeqId <- getAttrValue "id" -< nucleotideSequence
+    nucleotide_SeqName <- getAttrValue "name" -< nucleotideSequence
+    nucleotide_SeqLength <- getAttrValue "length" -< nucleotideSequence
+    nucleotide_SeqWeight <- getAttrValue "weight" -< nucleotideSequence
+    returnA -< Sequence {
+      sequenceId = nucleotide_SeqId, 
+      sequenceName = nucleotide_SeqName,
+      sequenceLength = read nucleotide_SeqLength :: Int,
+      sequenceWeight = read nucleotide_SeqWeight :: Double}
+
+-- | get a result motif
+getMotif :: ArrowXml a => a XmlTree Motif  
+getMotif = atTag "motif"  >>> 
+  proc mememotif -> do
+    motif_id <- getAttrValue "id" -< mememotif
+    motif_name <- getAttrValue "name" -< mememotif
+    motif_width <- getAttrValue "width" -< mememotif
+    motif_sites <- getAttrValue "sites" -< mememotif
+    motif_ic <- getAttrValue "ic" -< mememotif
+    motif_re <- getAttrValue "re" -< mememotif
+    motif_llr <- getAttrValue "llr" -< mememotif
+    motif_e_value <- getAttrValue "e_value" -< mememotif
+    motif_bayes_threshold <- getAttrValue "bayes_threshold" -< mememotif
+    motif_elapsed_time <- getAttrValue "elapsed_time" -< mememotif
+    motif_scores <- getScores -< mememotif
+    motif_propabilities <- getPropabilities -< mememotif
+    regex <- getText <<< getChildren <<<  atTag "regular_expression" -< mememotif
+    contributingsites <- listA getContributingSite -< mememotif
+    returnA -< Motif {
+      motifId = motif_id, 
+      motifName = motif_name,
+      motifWidth = read motif_width :: Int,
+      motifSites = read motif_sites :: Int,
+      motifIc = read motif_ic :: Double,
+      motifRe = read motif_re :: Double,
+      motifLlr = read motif_llr :: Int, 
+      motifEvalue = read motif_e_value :: Double,
+      motifBayesTreshold = read motif_bayes_threshold :: Double,
+      motifElapsedTime = read motif_elapsed_time :: Double,
+      -- regex field contains 2 linebreaks
+      motifRegularexpression = filter (/= '\n') regex,
+      motifScores = motif_scores,
+      motifProbabilites = motif_propabilities,
+      motifContributingsites = contributingsites }
+
+getScores :: ArrowXml a => a XmlTree Scores
+getScores = atTag "scores" >>>
+  proc memescores -> do
+  scores_alphabetmatrix <-getAlphabetMatrix  -< memescores
+  returnA -< Scores {
+    scoreAlphabetMatrix = scores_alphabetmatrix}
+
+getPropabilities :: ArrowXml a => a XmlTree Propabilities
+getPropabilities = atTag "propabilities" >>>
+  proc memepropabilities -> do
+  propabilities_alphabetmatrix <-getAlphabetMatrix  -< memepropabilities
+  returnA -< Propabilities {
+    propabilitiesAlphabetMatrix = propabilities_alphabetmatrix}
+
+getAlphabetMatrix :: ArrowXml a => a XmlTree AlphabetMatrix
+getAlphabetMatrix = atTag "alphabet_matrix" >>>
+  proc memeaalphabetmatrix -> do
+    alphabet_matrix <- listA getAlphabetArray -< memeaalphabetmatrix
+    returnA -< AlphabetMatrix {
+      alphabetMatrixArrays = alphabet_matrix} 
+   
+getContributingSite :: ArrowXml a => a XmlTree ContributingSite  
+getContributingSite = atTag "contributing_site" >>> 
+  proc contributingsite -> do
+  contributing_site_id <- getAttrValue "sequence_id" -< contributingsite
+  contributing_site_position <- getAttrValue "position" -< contributingsite
+  contributing_site_strand <- getAttrValue "strand" -< contributingsite
+  contributing_site_pvalue <- getAttrValue "pvalue" -< contributingsite
+  contributing_site_left_flank <- getText <<< getChildren <<< atTag "left_flank"  -< contributingsite
+  contributing_site <- getSite  -< contributingsite
+  contributing_site_right_flank <- getText <<< getChildren <<< atTag "right_flank"  -< contributingsite
+  returnA -<  ContributingSite {
+    contributingSiteId = contributing_site_id,
+    contributingSitePosition = read contributing_site_position :: Int,
+    contributingSiteStrand = contributing_site_strand,
+    contributingSitePvalue = read contributing_site_pvalue :: Double,
+    contributingSiteLeftFlank = contributing_site_left_flank,
+    contributingSite = contributing_site,
+    contributingSiteRightFlank = contributing_site_right_flank}
+
+getSite :: ArrowXml a => a XmlTree Site
+getSite = atTag "site" >>>
+   proc site -> do
+   site_letterreferences <- listA getSiteLetterReference -< site
+   returnA -< Site {
+     siteLetterReferences = site_letterreferences}
+ 
+getSiteLetterReference :: ArrowXml a => a XmlTree LetterReference
+getSiteLetterReference = atTag "letter_ref" >>>
+  proc letterreference -> do
+  letterid <- getAttrValue "letter_id" -< letterreference
+  returnA -< LetterReference {
+    letterReference = letterid}
+   
+getScannedSiteSummary :: ArrowXml a => a XmlTree ScannedSiteSummary
+getScannedSiteSummary = atTag "scanned_sites_summary" >>>
+  proc scannedsitesummary  -> do
+    scannedsitesummary_p_tresh <- getAttrValue "p_thresh" -< scannedsitesummary
+    scannedsites <- listA getScannedSites -< scannedsitesummary
+    returnA -< ScannedSiteSummary{
+      pThresh = read scannedsitesummary_p_tresh :: Double,
+      scannedSites = scannedsites}
+
+getScannedSites :: ArrowXml a => a XmlTree ScannedSites
+getScannedSites = atTag "scanned_sites" >>>
+  proc scannedsites  -> do
+    scannedsites_sequence_id <- getAttrValue "sequence_id" -< scannedsites
+    scannedsites_pvalue <- getAttrValue "pvalue" -< scannedsites
+    scannedsites_num_sites <- getAttrValue "num_sites" -< scannedsites       
+    scannedsites_array <- listA getScannedSite -< scannedsites
+    returnA -< ScannedSites{
+      scannedsitesSequenceId = scannedsites_sequence_id,
+      scannedSitesPvalue = read scannedsites_pvalue :: Double,
+      numSites = read scannedsites_num_sites :: Int,
+      scannedSiteArray = scannedsites_array}
+                               
+getScannedSite :: ArrowXml a => a XmlTree ScannedSite
+getScannedSite = atTag "scanned_site" >>>
+  proc scannedsite  -> do
+    scannedsite_motif_id <- getAttrValue "motif_id" -< scannedsite
+    scannedsite_strand <- getAttrValue "strand" -< scannedsite
+    scannedsite_position <- getAttrValue "position" -< scannedsite     
+    scannedsite_sitepvalue <- getAttrValue "pvalue" -< scannedsite
+    returnA -< ScannedSite{
+      scannedsiteMotifId = scannedsite_motif_id,
+      strand = scannedsite_strand,
+      position = read scannedsite_position :: Int,
+      scannedSitePvalue = read scannedsite_sitepvalue :: Double}