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:             0.6.3.0
+version:             0.7.0.0
 synopsis:            Return the diversity at each position for all sequences in a fasta file
 description:         Find the diversity of a collection of entities, mainly for use with fasta sequences. Produces a binary which works on fasta files to find the diversity of any order and rarefaction curves for a sliding window across all positions in the sequences. To analyze just a collection of entities, just use the whole sequences and list flag.
 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
@@ -28,6 +28,7 @@
                        , inputWindow            :: Int
                        , inputFasta             :: String
                        , inputSampleField       :: Int
+                       , inputCountField        :: Int
                        , inputSubsampling       :: String
                        , inputG                 :: Double
                        , fastBin                :: Bool
@@ -78,6 +79,17 @@
          <> value 1
          <> help "The index for the sample ID in the header separated by '|'\
                  \ (1 indexed)" )
+      <*> option auto
+          ( long "input-count-field"
+         <> short 'C'
+         <> metavar "INT"
+         <> value 0
+         <> help "The index for the number of this type in the header separated\
+                 \ by '|' (1 indexed). Used if there are multiple copies\
+                 \ of one entry, so a '4' in the header would indicate that\
+                 \ this entity occurred 4 times. Defaults to 0, meaning that\
+                 \ this field is ignored and count each sequence as occurring\
+                 \ just once" )
       <*> strOption
           ( long "input-subsampling"
          <> short 'I'
@@ -168,7 +180,7 @@
          <> metavar "FILE"
          <> value ""
          <> help "The csv file containing the diversities at each position.\
-                 \ expects a string, so you need a string wven with std" )
+                 \ expects a string, so you need a string even with std" )
 
 parseSampling :: (Num a, Read a) => String -> [a]
 parseSampling = map read . parsing . words
@@ -188,6 +200,7 @@
         >-> P.map ( generatePositionMap
                     (sample opts)
                     (inputSampleField opts)
+                    (inputCountField opts)
                     (wholeSeq opts)
                     (inputWindow opts)
                   . removals )
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
@@ -23,10 +23,15 @@
 -- Local
 import Math.Diversity.Types
 
--- | Get the sample ID of a sequence
-getSample :: Int -> FastaSequence -> Sample
-getSample x = (!! (x - 1)) . Split.splitOn "|" . fastaHeader
+-- | Get the field of a fasta sequence header
+getField :: Int -> FastaSequence -> String
+getField x = (!! (x - 1)) . Split.splitOn "|" . fastaHeader
 
+-- | Get the count field of a fasta sequence header
+getCount :: Int -> FastaSequence -> Int
+getCount 0 = const 1
+getCount x = read . getField x
+
 -- | Generates fragment list from string of "win" length. This version
 -- differs from normal as it takes a tuple with the position as the first
 -- entry. Is in tail recursive form
@@ -46,19 +51,23 @@
 -- | Generate the frequency from a FastaSequence
 generatePositionMap :: Bool
                     -> Int
+                    -> Int
                     -> Bool
                     -> Window
                     -> FastaSequence
                     -> PositionMap
-generatePositionMap !sample !sampleField !whole !win = posSeqList
+generatePositionMap !sample !sampleField !countField !whole !win = posSeqList
   where
     posSeqList !x       = Map.fromList
-                        . map (\(!p, !f) -> (p, Map.singleton (sampleIt sample x f) 1))
+                        . map ( \(!p, !f) -> ( p
+                                             , Map.singleton (sampleIt sample x f)
+                                             . getCount countField
+                                             $ x ) )
                         . fragmentPos whole win
                         . filter (noGaps . snd)
                         . zip [1..]
                         . fastaSeq
                         $ x
     noGaps y            = y /= '-' && y /= '.'
-    sampleIt True !s !f = (getSample sampleField s, f)
+    sampleIt True !s !f = (getField sampleField s, f)
     sampleIt False _ !f = ("Sample", f)