diff --git a/diversity.cabal b/diversity.cabal
--- a/diversity.cabal
+++ b/diversity.cabal
@@ -2,7 +2,7 @@
 -- documentation, see http://haskell.org/cabal/users-guide/
 
 name:                diversity
-version:             0.7.0.3
+version:             0.7.1.0
 synopsis:            Return the diversity at each position by default for all sequences in a fasta file
 description:         Find the diversity of a collection of entities, mainly for use with fasta sequences.
 homepage:            https://github.com/GregorySchwartz/diversity
diff --git a/src/src-exec/Main.hs b/src/src-exec/Main.hs
--- a/src/src-exec/Main.hs
+++ b/src/src-exec/Main.hs
@@ -33,6 +33,7 @@
                        , inputG                 :: Double
                        , fastBin                :: Bool
                        , runs                   :: Int
+                       , gapsFlag               :: Bool
                        , removeNBool            :: Bool
                        , wholeSeq               :: Bool
                        , list                   :: Bool
@@ -131,6 +132,13 @@
                  \ rarefaction is automatically enabled (individual based only,\
                  \ not for sample based)" )
       <*> switch
+          ( long "keep-gaps"
+         <> short 'G'
+         <> help "Do not remove '.' and '-' characters from the analysis. This\
+                 \ flag will thus treat these characters as additional entities\
+                 \ rather than be ignored as artificial biological gaps in\
+                 \ a sequence" )
+      <*> switch
           ( long "remove-N"
          <> short 'n'
          <> help "Remove 'N' and 'n' characters" )
@@ -198,6 +206,7 @@
           $ P.fromHandle h
         >-> toFastaSequence (list opts) h
         >-> P.map ( generatePositionMap
+                    (gapsFlag opts)
                     (sample opts)
                     (inputSampleField opts)
                     (inputCountField opts)
diff --git a/src/src-lib/Math/Diversity/GenerateDiversity.hs b/src/src-lib/Math/Diversity/GenerateDiversity.hs
--- a/src/src-lib/Math/Diversity/GenerateDiversity.hs
+++ b/src/src-lib/Math/Diversity/GenerateDiversity.hs
@@ -15,7 +15,6 @@
 import Data.List
 import Data.Fasta.String
 import qualified Data.Sequence as Seq
-import Debug.Trace
 
 -- Cabal
 import qualified Data.List.Split as Split
@@ -50,13 +49,15 @@
 
 -- | Generate the frequency from a FastaSequence
 generatePositionMap :: Bool
+                    -> Bool
                     -> Int
                     -> Int
                     -> Bool
                     -> Window
                     -> FastaSequence
                     -> PositionMap
-generatePositionMap !sample !sampleField !countField !whole !win = posSeqList
+generatePositionMap !gapsFlag !sample !sampleField !countField !whole !win =
+    posSeqList
   where
     posSeqList !x       = Map.fromList
                         . map ( \(!p, !f) -> ( p
@@ -68,6 +69,6 @@
                         . zip [1..]
                         . fastaSeq
                         $ x
-    noGaps y            = y /= '-' && y /= '.'
+    noGaps y            = (y /= '-' && y /= '.') || gapsFlag
     sampleIt True !s !f = (getField sampleField s, f)
     sampleIt False _ !f = ("Sample", f)