diff --git a/Biobase/TrainingData/Manip.hs b/Biobase/TrainingData/Manip.hs
--- a/Biobase/TrainingData/Manip.hs
+++ b/Biobase/TrainingData/Manip.hs
@@ -2,6 +2,9 @@
 
 module Biobase.TrainingData.Manip where
 
+import Data.List (sort,sortBy)
+import Data.Ord (comparing)
+
 import Biobase.Secondary.PseudoKnots
 
 import Biobase.TrainingData
@@ -17,3 +20,19 @@
 removePK rpk td@TrainingData{..}
   | not rpk   = td
   | otherwise = td{secondary = removeByCounting secondary}
+
+-- | Remove triplets from training data. "rmTs" will check each extPair and
+-- remove it, if it is the worst in a triplet. If not, the pair is rotated to
+-- the last position and we continue. In the non-triplet case, we simply remove
+-- the pair from consideration and put it into the output (x:).
+
+fRemoveTriplets False td = td
+fRemoveTriplets True td@TrainingData{..} = td{secondary = sort $ rmTs secondary} where
+  rmTs [] = []
+  rmTs (x:xs)
+    | ys <- triplets x xs
+    , not $ null ys = if worst x ys then rmTs xs else rmTs xs++[x]
+    | otherwise = x : rmTs xs
+    where
+      triplets ((i,j),_) zs = filter (\((k,l),_) -> i==k || i==l || j==k || j==l) zs
+      worst z zs = last (sortBy (comparing snd) $ z : zs) == z
diff --git a/BiobaseTrainingData.cabal b/BiobaseTrainingData.cabal
--- a/BiobaseTrainingData.cabal
+++ b/BiobaseTrainingData.cabal
@@ -1,5 +1,5 @@
 name:           BiobaseTrainingData
-version:        0.1.1.0
+version:        0.1.2.0
 author:         Christian Hoener zu Siederdissen
 maintainer:     choener@tbi.univie.ac.at
 homepage:       http://www.tbi.univie.ac.at/~choener/
diff --git a/MkTrainingData.hs b/MkTrainingData.hs
--- a/MkTrainingData.hs
+++ b/MkTrainingData.hs
@@ -30,6 +30,7 @@
     , fromdir   :: FilePath
     , errorFile :: Maybe FilePath
     , relativePairs :: Maybe Double
+    , removeTriplets :: Bool
     }
   -- | RNAstrand reads from one file
   | RNAstrand
@@ -45,6 +46,7 @@
   , fromdir   = "./"  &= args
   , errorFile = def   &= help "put TrainingData which falls through the filter in this file (default: disabled)"
   , relativePairs = def &= help "Keep only TrainingData with that fraction of basepairs."
+  , removeTriplets = False &= help "remove triplets pairs (tries to remove non-canonical part first) (default: disabled)"
   }
 
 rnastrand = RNAstrand
@@ -63,16 +65,15 @@
   let (ys :: [TDmanip]) = id
           . map (fErrorCheck)                 -- basic error-checking
           . map (fMinRelPairs relativePairs)  -- filtering out trainingdata with too few pairs
+          . map (fmap $ fRemoveTriplets removeTriplets)  -- removes triplet pairs (parts of)
           . map (fmap (removePK removepk))    -- remove pseudoknots from trainingdata
           . map (fmap (mkTrainingData . removeBIF . F.linearizeFR3D)) -- basic conversions
           . map Right
           $ xs
   let (ls,rs) = partition isLeft ys
+  mapM_ (print . fromRight) rs
   when (isJust errorFile) $ do
     writeFile (fromJust errorFile) . unlines . map (show . fromLeft) $ ls
-  mapM_ (print . fromRight) rs
-  return ()
-  -- mapM_ print $ map (removePK removepk . mkTrainingData . removeBIF . F.linearizeFR3D) xs
 
 -- | RNAstrand importer