diff --git a/LICENSE b/LICENSE
new file mode 100644
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,30 @@
+Copyright Biocad (c) 2017
+
+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 Bogdan Neterebskii 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/README.md b/README.md
new file mode 100644
--- /dev/null
+++ b/README.md
@@ -0,0 +1,2 @@
+# sequence
+TODO
diff --git a/Setup.hs b/Setup.hs
new file mode 100644
--- /dev/null
+++ b/Setup.hs
@@ -0,0 +1,2 @@
+import Distribution.Simple
+main = defaultMain
diff --git a/bio-sequence.cabal b/bio-sequence.cabal
new file mode 100644
--- /dev/null
+++ b/bio-sequence.cabal
@@ -0,0 +1,70 @@
+name:                bio-sequence
+version:             0.1.0.0
+synopsis:            Initial project template from stack
+description:         Please see README.md
+homepage:            https://github.com/biocad/bio-sequence
+license:             BSD3
+license-file:        LICENSE
+author:              Pavel Yakovlev
+maintainer:          yakovlev@biocad.ru
+copyright:           Copyright: (c) 2017 Biocad
+category:            Bio
+build-type:          Simple
+extra-source-files:  README.md
+cabal-version:       >=1.10
+
+library
+  hs-source-dirs:      src
+  exposed-modules:     Bio.Sequence
+                     , Bio.Sequence.Alignment
+                     , Bio.Sequence.Alignment.Matrix
+                     , Bio.Sequence.Alignment.Scoring
+                     , Bio.Sequence.AminoAcid
+                     , Bio.Sequence.Parser.Fasta
+                     , Bio.Macro
+  other-modules:       Bio.Sequence.Alignment.Internal.Type
+                     , Bio.Sequence.Alignment.Internal.Instances
+                     , Bio.Sequence.Alignment.Internal.Matrix.Scoring
+                     , Bio.Sequence.Alignment.Internal.Matrix.Template
+                     , Bio.Sequence.Alignment.Scoring.Similarity
+                     , Bio.Sequence.AminoAcid.Internal.Types
+                     , Bio.Sequence.Parser.Fasta.Internal.Parser
+                     , Bio.Sequence.Parser.Fasta.Internal.Converters
+                     , Bio.Macro.Internal.Instances
+                     , Bio.Macro.Internal.Types
+  build-depends:       base >= 4.7 && < 5
+                     , bytestring
+                     , array
+                     , template-haskell
+                     , text
+                     , parsec
+  ghc-options:         -Wall -O2
+  default-language:    Haskell2010
+
+test-suite sequence-test
+  type:                exitcode-stdio-1.0
+  hs-source-dirs:      test
+  main-is:             Spec.hs
+  build-depends:       base
+                     , bio-sequence
+                     , bytestring
+                     , hspec
+                     , QuickCheck
+  ghc-options:         -threaded -rtsopts -with-rtsopts=-N
+  default-language:    Haskell2010
+
+test-suite similarity
+  type:                exitcode-stdio-1.0
+  hs-source-dirs:      test
+  main-is:             SpecSimilarity.hs
+  build-depends:       base
+                     , bio-sequence
+                     , bytestring
+                     , hspec
+                     , QuickCheck
+  ghc-options:         -threaded -rtsopts -with-rtsopts=-N
+  default-language:    Haskell2010
+
+source-repository head
+  type:     git
+  location: https://github.com/biocad/bio-sequence
diff --git a/src/Bio/Macro.hs b/src/Bio/Macro.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Macro.hs
@@ -0,0 +1,7 @@
+module Bio.Macro
+  ( MacroMolecule (..), Chain (..)
+
+  ) where
+
+import           Bio.Macro.Internal.Instances ()
+import           Bio.Macro.Internal.Types     (Chain (..), MacroMolecule (..))
diff --git a/src/Bio/Macro/Internal/Instances.hs b/src/Bio/Macro/Internal/Instances.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Macro/Internal/Instances.hs
@@ -0,0 +1,14 @@
+{-# OPTIONS_GHC -fno-warn-orphans #-}
+
+module Bio.Macro.Internal.Instances
+  (
+
+  ) where
+
+import           Bio.Macro.Internal.Types (Chain (..), MacroMolecule (..))
+
+instance Functor (MacroMolecule a) where
+  fmap f mm = mm { mmChains = (f <$>) <$> mmChains mm }
+
+instance Functor (Chain t) where
+  fmap f ch = ch { chainResidues = f <$> chainResidues ch }
diff --git a/src/Bio/Macro/Internal/Types.hs b/src/Bio/Macro/Internal/Types.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Macro/Internal/Types.hs
@@ -0,0 +1,15 @@
+module Bio.Macro.Internal.Types
+  ( MacroMolecule (..)
+  , Chain (..)
+
+  ) where
+
+data MacroMolecule a r = MacroMolecule { mmName   :: !String
+                                       , mmChains :: ![Chain a r]
+                                       }
+  deriving (Show, Eq)
+
+data Chain t r = Chain { chainType     :: !t
+                       , chainResidues :: ![r]
+                       }
+  deriving (Show, Eq)
diff --git a/src/Bio/Sequence.hs b/src/Bio/Sequence.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Sequence.hs
@@ -0,0 +1,9 @@
+module Bio.Sequence
+  ( Sequence
+  , Chain (..)
+  ) where
+
+import           Bio.Macro (Chain (..))
+import           Data.Text (Text)
+
+type Sequence = Chain Text
diff --git a/src/Bio/Sequence/Alignment.hs b/src/Bio/Sequence/Alignment.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Sequence/Alignment.hs
@@ -0,0 +1,59 @@
+{-# LANGUAGE RecordWildCards #-}
+{-# LANGUAGE BangPatterns #-}
+{-# OPTIONS_GHC -fno-warn-incomplete-patterns -fno-warn-name-shadowing #-}
+
+module Bio.Sequence.Alignment
+    ( Substitution, Gap, Alignment (..)
+    , alignment
+    , mkGlobal, mkLocal, mkSemiglobal, mkEditDistance
+    ) where
+
+import           Data.Array                   (array, range, (!))
+import           Data.ByteString.Char8        (ByteString)
+import qualified Data.ByteString.Char8        as B
+
+import           Bio.Sequence.Alignment.Internal.Instances
+import           Bio.Sequence.Alignment.Internal.Type
+
+alignment :: Alignment a => a -> ByteString -> ByteString -> (Int, (ByteString, ByteString))
+alignment sa s t = (score, trace sm sn si ti)
+  where (m, n) = (B.length s, B.length t)
+        bounds = ((0, 0), (m, n))
+
+        (needGaps, (sm, sn)) = selector sa matrix
+        (si, ti) = if needGaps then tails else ([], [])
+
+        score = matrix ! (sm, sn)
+        gapSymbol = '-'
+
+        tails :: (String, String)
+        tails | m == sm = (gaps (n - sn), B.unpack (B.drop sn t))
+              | n == sn = (B.unpack (B.drop sm s), gaps (m - sm))
+
+        gaps :: Int -> String
+        gaps size = replicate size gapSymbol
+
+        distance :: Int -> Int -> Int
+        distance i 0 = inits sa i
+        distance 0 j = inits sa j
+        distance i j = maximum [ matrix ! (i - 1, j - 1) + sub i j
+                               , matrix ! (i - 1, j) + g
+                               , matrix ! (i, j - 1) + g
+                               , additional sa
+                               ]
+          where !g = gap sa
+
+        sub :: Substitution Int
+        sub = subIJ sa s t
+
+        matrix :: Matrix
+        !matrix = array bounds [(ij, uncurry distance ij) | ij <- range bounds]
+
+        trace :: Int -> Int -> String -> String -> (ByteString, ByteString)
+        trace i j s' t' | isStop  matrix s t i j = (B.pack s', B.pack t')
+                        | isVert  matrix s t i j = trace (i - 1) j (addToS i) (gapSymbol:t')
+                        | isHoriz matrix s t i j = trace i (j - 1) (gapSymbol:s') (addToT j)
+                        | isDiag  matrix s t i j = trace (i - 1) (j - 1) (addToS i) (addToT j)
+          where addToS i = (s `B.index` (i - 1)):s'
+                addToT j = (t `B.index` (j - 1)):t'
+                Conditions {..} = conditions sa
diff --git a/src/Bio/Sequence/Alignment/Internal/Instances.hs b/src/Bio/Sequence/Alignment/Internal/Instances.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Sequence/Alignment/Internal/Instances.hs
@@ -0,0 +1,116 @@
+{-# LANGUAGE BangPatterns  #-}
+{-# LANGUAGE TupleSections #-}
+{-# OPTIONS_GHC -fno-warn-incomplete-patterns -fno-warn-unused-matches #-}
+
+module Bio.Sequence.Alignment.Internal.Instances where
+
+import           Control.Monad                        (ap)
+import           Data.Array                           (assocs, bounds, (!))
+import           Data.ByteString.Char8                (ByteString)
+import qualified Data.ByteString.Char8                as B
+import           Data.List                            (maximumBy)
+
+import           Bio.Sequence.Alignment.Internal.Type
+
+data EditDistance = EditDistance
+
+data AlignmentType = GlobalAlignment
+                   | LocalAlignment
+                   | SemiglobalAlignment
+  deriving (Show, Eq)
+
+data SimpleAlignment = SimpleAlignment { aType :: AlignmentType
+                                       , subst :: Substitution Char
+                                       , aGap  :: Gap
+                                       }
+
+instance Alignment EditDistance where
+  gap _ = -1
+  substitution _ c d | c == d    = 0
+                     | otherwise = -1
+  conditions = defaultConds
+  selector ed mat = let (_, sp) = bounds mat in (True, sp)
+  inits ed = (* gap ed)
+  additional _ = minBound
+
+instance Alignment SimpleAlignment where
+  gap = aGap
+  substitution = subst
+  conditions sa | aType sa == LocalAlignment      = localConds sa
+                | aType sa == SemiglobalAlignment = semiConds sa
+                | otherwise                       = defaultConds sa
+  selector sa mat | aType sa == GlobalAlignment     = (False, snd $ bounds mat)
+                  | aType sa == LocalAlignment      = (False, localStart mat)
+                  | aType sa == SemiglobalAlignment = (True, semiglobalStart mat)
+  inits sa | aType sa == GlobalAlignment = (* gap sa)
+           | otherwise                   = const 0
+  additional sa | aType sa == LocalAlignment = 0
+                | otherwise                  = minBound
+
+mkGlobal :: Substitution Char -> Gap -> SimpleAlignment
+mkGlobal = SimpleAlignment GlobalAlignment
+
+mkLocal :: Substitution Char -> Gap -> SimpleAlignment
+mkLocal = SimpleAlignment LocalAlignment
+
+mkSemiglobal :: Substitution Char -> Gap -> SimpleAlignment
+mkSemiglobal = SimpleAlignment SemiglobalAlignment
+
+mkEditDistance :: EditDistance
+mkEditDistance = EditDistance
+
+
+-- Default helpers
+
+subIJ :: Alignment a => a -> ByteString -> ByteString -> Substitution Int
+subIJ sa s t i j = sub (s `B.index` (i - 1)) (t `B.index` (j - 1))
+  where !sub = substitution sa
+{-# INLINE subIJ #-}
+
+localStart :: Matrix -> (Int, Int)
+localStart = listKeyByValMax . assocs
+
+semiglobalStart :: Matrix -> (Int, Int)
+semiglobalStart mat = listKeyByValMax $ lastRow ++ lastCol
+  where lastRow = ap (,) (mat !) . (me,) <$> [ns..ne]
+        lastCol = ap (,) (mat !) . (,ne) <$> [ms..me]
+        ((ms, ns), (me, ne)) = bounds mat
+
+localConds :: Alignment a => a -> Conditions
+localConds a = (defaultConds a) { isStop = localStop a }
+
+defaultConds :: Alignment a => a -> Conditions
+defaultConds a = Conditions { isStop = defaultStop a
+                            , isDiag = defaultDiag a
+                            , isVert = defaultVert a
+                            , isHoriz = defaultHoriz a
+                            }
+
+semiConds :: Alignment a => a -> Conditions
+semiConds a = Conditions { isStop = defaultStop a
+                         , isDiag = defaultDiag a
+                         , isVert = \m s t i j -> j == 0 || (i /= 0 && m ! (i, j) == m ! (i - 1, j) + gap a)
+                         , isHoriz = \m s t i j -> i == 0 || (j /= 0 && m ! (i, j) == m ! (i, j - 1) + gap a)
+                         }
+
+localStop :: Alignment a => a -> Condition
+localStop _ m _ _ i j = i == 0 || j == 0 || m ! (i, j) == 0
+
+defaultStop :: Alignment a => a -> Condition
+defaultStop _ _ _ _ i j = i == 0 && j == 0
+
+defaultDiag :: Alignment a => a -> Condition
+defaultDiag sa m s t i j = i /= 0 && j /= 0 && m ! (i, j) == m ! (i - 1, j - 1) + sub i j
+  where sub = subIJ sa s t
+
+defaultVert :: Alignment a => a -> Condition
+defaultVert sa m s t i j = i /= 0 && m ! (i, j) == m ! (i - 1, j) + gap sa
+
+defaultHoriz :: Alignment a => a -> Condition
+defaultHoriz sa m s t i j = j /= 0 && m ! (i, j) == m ! (i, j - 1) + gap sa
+
+listKeyByValMax :: Ord b => [(a, b)] -> a
+listKeyByValMax = fst . maximumBy elemsOrd
+  where elemsOrd (_, x) (_, y) | x == y = EQ
+                               | x <  y = LT
+                               | x >  y = GT
diff --git a/src/Bio/Sequence/Alignment/Internal/Matrix/Scoring.hs b/src/Bio/Sequence/Alignment/Internal/Matrix/Scoring.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Sequence/Alignment/Internal/Matrix/Scoring.hs
@@ -0,0 +1,23 @@
+{-# LANGUAGE BangPatterns #-}
+{-# OPTIONS_GHC -fno-warn-incomplete-patterns -fno-warn-name-shadowing #-}
+
+module Bio.Sequence.Alignment.Internal.Matrix.Scoring where
+
+import           Control.Applicative                  (liftA2)
+import           Data.List                            (words)
+
+import           Bio.Sequence.Alignment.Internal.Type
+
+class ScoringMatrix a where
+  scoring :: a -> Substitution Char
+
+loadMatrix :: String -> [((Char, Char), Int)]
+loadMatrix txt = concat table
+  where f = liftA2 (||) null ((/= '#') . head)
+        strip = reverse . dropWhile (== ' ') . reverse . dropWhile (== ' ')
+        !txtlns = filter f (strip <$> lines txt)
+        !letters = (map head . words . head) txtlns
+        !table = (map (lineMap . words) . tail) txtlns
+        lineMap (x:xs) = let !hx = head x
+                             f (n, c) = ((hx, c), n)
+                         in f <$> (read <$> xs) `zip` letters
diff --git a/src/Bio/Sequence/Alignment/Internal/Matrix/Template.hs b/src/Bio/Sequence/Alignment/Internal/Matrix/Template.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Sequence/Alignment/Internal/Matrix/Template.hs
@@ -0,0 +1,51 @@
+{-# LANGUAGE TemplateHaskell #-}
+
+module Bio.Sequence.Alignment.Internal.Matrix.Template where
+
+import           Data.Char                         (toLower)
+import           Language.Haskell.TH
+import           Language.Haskell.TH.Quote
+
+import           Bio.Sequence.Alignment.Internal.Type
+import           Bio.Sequence.Alignment.Internal.Matrix.Scoring
+
+matrix :: QuasiQuoter
+matrix = QuasiQuoter { quotePat = undefined
+                     , quoteType = undefined
+                     , quoteExp = undefined
+                     , quoteDec = matrixDec
+                     }
+
+
+matrixDec :: String -> Q [Dec]
+matrixDec s = do let slines = lines s
+                 let txt = (unlines . tail) slines
+                 let name = head slines
+                 (typeName, dataDecl) <- typeDec name
+                 (funcName, funDecls) <- functionDec name txt
+                 smDecl <- instDec typeName funcName
+                 return $ dataDecl : smDecl : funDecls
+
+instDec :: Name -> Name -> Q Dec
+instDec typeN funN = return $ decl [body]
+  where decl = InstanceD Nothing [] (AppT (ConT ''ScoringMatrix) (ConT typeN))
+        body = FunD 'scoring [Clause [WildP] (NormalB (VarE funN)) []]
+
+typeDec :: String -> Q (Name, Dec)
+typeDec name = do typeN <- newName name
+                  let dataN = mkName (nameBase typeN)
+                  let dervs = [ConT ''Show, ConT ''Eq]
+                  return (typeN, DataD [] typeN [] Nothing [NormalC dataN []] dervs)
+
+functionDec :: String -> String -> Q (Name, [Dec])
+functionDec name txt = do let subM = loadMatrix txt
+                          funName <- newName (toLower <$> name)
+                          let funSign = SigD funName (AppT (ConT ''Substitution) (ConT ''Char))
+                          let clauses = mkClause <$> subM
+                          let funDecl = FunD funName clauses
+                          return (funName, [funSign, funDecl])
+
+mkClause :: ((Char, Char), Int) -> Clause
+mkClause ((c, d), i) = Clause [litC c, litC d] (NormalB (litI i)) []
+  where litC = LitP . CharL
+        litI = LitE . IntegerL . fromIntegral
diff --git a/src/Bio/Sequence/Alignment/Internal/Type.hs b/src/Bio/Sequence/Alignment/Internal/Type.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Sequence/Alignment/Internal/Type.hs
@@ -0,0 +1,35 @@
+module Bio.Sequence.Alignment.Internal.Type where
+
+import           Data.Array     (Array)
+import Data.ByteString.Char8    (ByteString)
+
+-- |Represents alignment matrix
+type Matrix = Array (Int, Int) Int
+
+-- |Substitution function for 'a' values comparison
+type Substitution a = a -> a -> Int
+
+-- |Gap type
+type Gap = Int
+
+-- |Condition, that gets matrix, 'i' and 'j'
+type Condition = Matrix -> ByteString -> ByteString -> Int -> Int -> Bool
+
+-- |A set of traceback conditions
+data Conditions = Conditions { isStop  :: Condition -- ^Should we stop?
+                             , isDiag  :: Condition -- ^Should we go daigonally?
+                             , isVert  :: Condition -- ^Should we go vertically?
+                             , isHoriz :: Condition -- ^Should we go horizontally?
+                             }
+
+-- |Traceback starting point selector function, bool indicate if we have to add gaps to sequence
+type StartSelector = Matrix -> (Bool, (Int, Int))
+
+-- |Introduces all useful methods to create an alignment
+class Alignment a where
+  gap :: a -> Gap
+  substitution :: a -> Substitution Char
+  conditions :: a -> Conditions
+  inits :: a -> Int -> Int
+  selector :: a -> StartSelector
+  additional :: a -> Int
diff --git a/src/Bio/Sequence/Alignment/Matrix.hs b/src/Bio/Sequence/Alignment/Matrix.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Sequence/Alignment/Matrix.hs
@@ -0,0 +1,110 @@
+{-# LANGUAGE QuasiQuotes     #-}
+{-# LANGUAGE TemplateHaskell #-}
+
+module Bio.Sequence.Alignment.Matrix
+    ( ScoringMatrix (..)
+    , BLOSUM62 (..), PAM250 (..), NUC44 (..)
+    , blosum62, pam250, nuc44
+    , matrix
+    ) where
+
+import Bio.Sequence.Alignment.Internal.Matrix.Scoring
+import Bio.Sequence.Alignment.Internal.Matrix.Template
+
+[matrix|BLOSUM62
+#  Matrix made by matblas from blosum62.iij
+#  * column uses minimum score
+#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+#  Blocks Database = /data/blocks_5.0/blocks.dat
+#  Cluster Percentage: >= 62
+#  Entropy =   0.6979, Expected =  -0.5209
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1  0 -4
+R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1  0 -1 -4
+N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  3  0 -1 -4
+D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4  1 -1 -4
+C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4
+Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0  3 -1 -4
+E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4
+G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -4
+H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0  0 -1 -4
+I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3 -3 -1 -4
+L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4 -3 -1 -4
+K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0  1 -1 -4
+M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3 -1 -1 -4
+F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3 -3 -1 -4
+P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -1 -2 -4
+S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0  0  0 -4
+T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1  0 -4
+W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -3 -2 -4
+Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -2 -1 -4
+V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3 -2 -1 -4
+B -2 -1  3  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4  1 -1 -4
+Z -1  0  0  1 -3  3  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4
+X  0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2  0  0 -2 -1 -1 -1 -1 -1 -4
+* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1
+|]
+
+[matrix|PAM250
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -0.844, Entropy = 0.354 bits
+#
+# Lowest score = -8, Highest score = 17
+#
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  2 -2  0  0 -2  0  0  1 -1 -1 -2 -1 -1 -3  1  1  1 -6 -3  0  0  0  0 -8
+R -2  6  0 -1 -4  1 -1 -3  2 -2 -3  3  0 -4  0  0 -1  2 -4 -2 -1  0 -1 -8
+N  0  0  2  2 -4  1  1  0  2 -2 -3  1 -2 -3  0  1  0 -4 -2 -2  2  1  0 -8
+D  0 -1  2  4 -5  2  3  1  1 -2 -4  0 -3 -6 -1  0  0 -7 -4 -2  3  3 -1 -8
+C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3  0 -2 -8  0 -2 -4 -5 -3 -8
+Q  0  1  1  2 -5  4  2 -1  3 -2 -2  1 -1 -5  0 -1 -1 -5 -4 -2  1  3 -1 -8
+E  0 -1  1  3 -5  2  4  0  1 -2 -3  0 -2 -5 -1  0  0 -7 -4 -2  3  3 -1 -8
+G  1 -3  0  1 -3 -1  0  5 -2 -3 -4 -2 -3 -5  0  1  0 -7 -5 -1  0  0 -1 -8
+H -1  2  2  1 -3  3  1 -2  6 -2 -2  0 -2 -2  0 -1 -1 -3  0 -2  1  2 -1 -8
+I -1 -2 -2 -2 -2 -2 -2 -3 -2  5  2 -2  2  1 -2 -1  0 -5 -1  4 -2 -2 -1 -8
+L -2 -3 -3 -4 -6 -2 -3 -4 -2  2  6 -3  4  2 -3 -3 -2 -2 -1  2 -3 -3 -1 -8
+K -1  3  1  0 -5  1  0 -2  0 -2 -3  5  0 -5 -1  0  0 -3 -4 -2  1  0 -1 -8
+M -1  0 -2 -3 -5 -1 -2 -3 -2  2  4  0  6  0 -2 -2 -1 -4 -2  2 -2 -2 -1 -8
+F -3 -4 -3 -6 -4 -5 -5 -5 -2  1  2 -5  0  9 -5 -3 -3  0  7 -1 -4 -5 -2 -8
+P  1  0  0 -1 -3  0 -1  0  0 -2 -3 -1 -2 -5  6  1  0 -6 -5 -1 -1  0 -1 -8
+S  1  0  1  0  0 -1  0  1 -1 -1 -3  0 -2 -3  1  2  1 -2 -3 -1  0  0  0 -8
+T  1 -1  0  0 -2 -1  0  0 -1  0 -2  0 -1 -3  0  1  3 -5 -3  0  0 -1  0 -8
+W -6  2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4  0 -6 -2 -5 17  0 -6 -5 -6 -4 -8
+Y -3 -4 -2 -4  0 -4 -4 -5  0 -1 -1 -4 -2  7 -5 -3 -3  0 10 -2 -3 -4 -2 -8
+V  0 -2 -2 -2 -2 -2 -2 -1 -2  4  2 -2  2 -1 -1 -1  0 -6 -2  4 -2 -2 -1 -8
+B  0 -1  2  3 -4  1  3  0  1 -2 -3  1 -2 -4 -1  0  0 -5 -3 -2  3  2 -1 -8
+Z  0  0  1  3 -5  3  3  0  2 -2 -3  0 -2 -5  0  0 -1 -6 -4 -2  2  3 -1 -8
+X  0 -1  0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1  0  0 -4 -2 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8  1
+|]
+
+[matrix|NUC44
+#
+# This matrix was created by Todd Lowe   12/10/92
+#
+# Uses ambiguous nucleotide codes, probabilities rounded to
+#  nearest integer
+#
+# Lowest score = -4, Highest score = 5
+#
+    A   T   G   C   S   W   R   Y   K   M   B   V   H   D   N
+A   5  -4  -4  -4  -4   1   1  -4  -4   1  -4  -1  -1  -1  -2
+T  -4   5  -4  -4  -4   1  -4   1   1  -4  -1  -4  -1  -1  -2
+G  -4  -4   5  -4   1  -4   1  -4   1  -4  -1  -1  -4  -1  -2
+C  -4  -4  -4   5   1  -4  -4   1  -4   1  -1  -1  -1  -4  -2
+S  -4  -4   1   1  -1  -4  -2  -2  -2  -2  -1  -1  -3  -3  -1
+W   1   1  -4  -4  -4  -1  -2  -2  -2  -2  -3  -3  -1  -1  -1
+R   1  -4   1  -4  -2  -2  -1  -4  -2  -2  -3  -1  -3  -1  -1
+Y  -4   1  -4   1  -2  -2  -4  -1  -2  -2  -1  -3  -1  -3  -1
+K  -4   1   1  -4  -2  -2  -2  -2  -1  -4  -1  -3  -3  -1  -1
+M   1  -4  -4   1  -2  -2  -2  -2  -4  -1  -3  -1  -1  -3  -1
+B  -4  -1  -1  -1  -1  -3  -3  -1  -1  -3  -1  -2  -2  -2  -1
+V  -1  -4  -1  -1  -1  -3  -1  -3  -3  -1  -2  -1  -2  -2  -1
+H  -1  -1  -4  -1  -3  -1  -3  -1  -3  -1  -2  -2  -1  -2  -1
+D  -1  -1  -1  -4  -3  -1  -1  -3  -1  -3  -2  -2  -2  -1  -1
+N  -2  -2  -2  -2  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1
+|]
diff --git a/src/Bio/Sequence/Alignment/Scoring.hs b/src/Bio/Sequence/Alignment/Scoring.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Sequence/Alignment/Scoring.hs
@@ -0,0 +1,12 @@
+module Bio.Sequence.Alignment.Scoring
+  ( similarity
+  , hamming
+  , relativeHamming
+  , alignmentScore
+  , alignmentSemiglobalScore
+  ) where
+
+import           Bio.Sequence.Alignment.Scoring.Similarity (alignmentScore, alignmentSemiglobalScore,
+                                                            hamming,
+                                                            relativeHamming,
+                                                            similarity)
diff --git a/src/Bio/Sequence/Alignment/Scoring/Similarity.hs b/src/Bio/Sequence/Alignment/Scoring/Similarity.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Sequence/Alignment/Scoring/Similarity.hs
@@ -0,0 +1,34 @@
+module Bio.Sequence.Alignment.Scoring.Similarity
+  ( similarity
+  , hamming
+  , relativeHamming
+  , alignmentScore
+  , alignmentSemiglobalScore
+  ) where
+
+import           Data.ByteString.Char8         (ByteString)
+import qualified Data.ByteString.Char8         as B
+
+import           Bio.Sequence.Alignment        (Substitution, alignment,
+                                                mkGlobal, mkSemiglobal)
+import           Bio.Sequence.Alignment.Matrix (blosum62)
+
+similarity :: ByteString -> ByteString -> Float
+similarity f s = 1 - fromIntegral (hamming f' s') / fromIntegral (B.length f')
+  where (_, (f', s')) = alignment (mkGlobal blosum62 (-5)) f s
+
+hamming :: ByteString -> ByteString -> Int
+hamming f s = sum $ B.zipWith notTheSame f s
+  where
+    notTheSame :: Char -> Char -> Int
+    notTheSame f' s' = if f' /= s' then 1 else 0
+
+relativeHamming :: ByteString -> ByteString -> Float
+relativeHamming f s = fromIntegral hammingValue / fromIntegral (B.length f)
+  where hammingValue = hamming f s
+
+alignmentScore :: Substitution Char -> ByteString -> ByteString -> Int
+alignmentScore matrix f s = fst $ alignment (mkGlobal matrix (-5)) f s
+
+alignmentSemiglobalScore :: Substitution Char -> ByteString -> ByteString -> Int
+alignmentSemiglobalScore matrix f s = fst $ alignment (mkSemiglobal matrix (-5)) f s
diff --git a/src/Bio/Sequence/AminoAcid.hs b/src/Bio/Sequence/AminoAcid.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Sequence/AminoAcid.hs
@@ -0,0 +1,8 @@
+module Bio.Sequence.AminoAcid
+  ( AminoAcid (..)
+  , shortName3, shortName, fromChar, fromShortCode
+  ) where
+
+import           Bio.Sequence.AminoAcid.Internal.Types (AminoAcid (..),
+                                                        fromChar, fromShortCode,
+                                                        shortName, shortName3)
diff --git a/src/Bio/Sequence/AminoAcid/Internal/Types.hs b/src/Bio/Sequence/AminoAcid/Internal/Types.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Sequence/AminoAcid/Internal/Types.hs
@@ -0,0 +1,112 @@
+module Bio.Sequence.AminoAcid.Internal.Types
+  ( AminoAcid (..)
+  , shortName3, shortName, fromChar, fromShortCode
+  ) where
+
+import           Data.Char (toUpper)
+
+data AminoAcid = Alanine | Glycine | Valine | Isoleucine | Leucine | Methionine
+               | Phenylalanine | Tyrosine | Tryptophan | Serine | Threonine
+               | Asparagine | Glutamine | Cysteine | Proline | Arginine
+               | Histidine | Lysine | AsparticAcid | GlutamicAcid
+               | AcetylGroup | MetilAmine
+  deriving (Show, Read, Eq, Ord)
+
+shortName3 :: AminoAcid -> String
+shortName3 Alanine       = "Ala"
+shortName3 Glycine       = "Gly"
+shortName3 Valine        = "Val"
+shortName3 Isoleucine    = "Ile"
+shortName3 Leucine       = "Leu"
+shortName3 Methionine    = "Met"
+shortName3 Phenylalanine = "Phe"
+shortName3 Tyrosine      = "Tyr"
+shortName3 Tryptophan    = "Trp"
+shortName3 Serine        = "Ser"
+shortName3 Threonine     = "Thr"
+shortName3 Asparagine    = "Asn"
+shortName3 Glutamine     = "Gln"
+shortName3 Cysteine      = "Cys"
+shortName3 Proline       = "Pro"
+shortName3 Arginine      = "Arg"
+shortName3 Histidine     = "His"
+shortName3 Lysine        = "Lys"
+shortName3 AsparticAcid  = "Asp"
+shortName3 GlutamicAcid  = "Glu"
+shortName3 AcetylGroup   = "Ace"
+shortName3 MetilAmine    = "Nma"
+
+shortName :: AminoAcid -> Char
+shortName Alanine       = 'A'
+shortName Glycine       = 'G'
+shortName Valine        = 'V'
+shortName Isoleucine    = 'I'
+shortName Leucine       = 'L'
+shortName Methionine    = 'M'
+shortName Phenylalanine = 'F'
+shortName Tyrosine      = 'Y'
+shortName Tryptophan    = 'W'
+shortName Serine        = 'S'
+shortName Threonine     = 'T'
+shortName Asparagine    = 'N'
+shortName Glutamine     = 'Q'
+shortName Cysteine      = 'C'
+shortName Proline       = 'P'
+shortName Arginine      = 'R'
+shortName Histidine     = 'H'
+shortName Lysine        = 'K'
+shortName AsparticAcid  = 'D'
+shortName GlutamicAcid  = 'E'
+shortName AcetylGroup   = '^'
+shortName MetilAmine    = '$'
+
+fromShortCode :: String -> AminoAcid
+fromShortCode str = fromCode' $ toUpper <$> str
+  where fromCode' "ALA" = Alanine
+        fromCode' "GLY" = Glycine
+        fromCode' "VAL" = Valine
+        fromCode' "ILE" = Isoleucine
+        fromCode' "LEU" = Leucine
+        fromCode' "MET" = Methionine
+        fromCode' "PHE" = Phenylalanine
+        fromCode' "TYR" = Tyrosine
+        fromCode' "TRP" = Tryptophan
+        fromCode' "SER" = Serine
+        fromCode' "THR" = Threonine
+        fromCode' "ASN" = Asparagine
+        fromCode' "GLN" = Glutamine
+        fromCode' "CYS" = Cysteine
+        fromCode' "PRO" = Proline
+        fromCode' "ARG" = Arginine
+        fromCode' "HIS" = Histidine
+        fromCode' "LYS" = Lysine
+        fromCode' "ASP" = AsparticAcid
+        fromCode' "GLU" = GlutamicAcid
+        fromCode' "ACE" = AcetylGroup
+        fromCode' "NMA" = MetilAmine
+        fromCode' code  = error $ "Unknown aminoacid code => " ++ code
+
+fromChar :: Char -> AminoAcid
+fromChar 'A'  = Alanine
+fromChar 'G'  = Glycine
+fromChar 'V'  = Valine
+fromChar 'I'  = Isoleucine
+fromChar 'L'  = Leucine
+fromChar 'M'  = Methionine
+fromChar 'F'  = Phenylalanine
+fromChar 'Y'  = Tyrosine
+fromChar 'W'  = Tryptophan
+fromChar 'S'  = Serine
+fromChar 'T'  = Threonine
+fromChar 'N'  = Asparagine
+fromChar 'Q'  = Glutamine
+fromChar 'C'  = Cysteine
+fromChar 'P'  = Proline
+fromChar 'R'  = Arginine
+fromChar 'H'  = Histidine
+fromChar 'K'  = Lysine
+fromChar 'D'  = AsparticAcid
+fromChar 'E'  = GlutamicAcid
+fromChar '^'  = AcetylGroup
+fromChar '$'  = MetilAmine
+fromChar code = error $ "Unknown aminoacid code => " ++ [code]
diff --git a/src/Bio/Sequence/Parser/Fasta.hs b/src/Bio/Sequence/Parser/Fasta.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Sequence/Parser/Fasta.hs
@@ -0,0 +1,7 @@
+module Bio.Sequence.Parser.Fasta
+  ( fastaParser
+  , aminoParser
+  ) where
+
+import           Bio.Sequence.Parser.Fasta.Internal.Converters (aminoParser)
+import           Bio.Sequence.Parser.Fasta.Internal.Parser     (fastaParser)
diff --git a/src/Bio/Sequence/Parser/Fasta/Internal/Converters.hs b/src/Bio/Sequence/Parser/Fasta/Internal/Converters.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Sequence/Parser/Fasta/Internal/Converters.hs
@@ -0,0 +1,17 @@
+module Bio.Sequence.Parser.Fasta.Internal.Converters
+  ( aminoParser
+
+  ) where
+
+import           Bio.Sequence                              (Chain (..),
+                                                            Sequence)
+import           Bio.Sequence.AminoAcid                    (AminoAcid (..),
+                                                            fromChar)
+import           Bio.Sequence.Parser.Fasta.Internal.Parser (fastaParser)
+import           Text.Parsec.Text                          (Parser)
+
+aminoParser :: Parser [Sequence AminoAcid]
+aminoParser = (charSeqToAminoSeq <$>) <$> fastaParser
+
+charSeqToAminoSeq :: Sequence Char -> Sequence AminoAcid
+charSeqToAminoSeq (Chain name residues) = Chain name (fromChar <$> residues)
diff --git a/src/Bio/Sequence/Parser/Fasta/Internal/Parser.hs b/src/Bio/Sequence/Parser/Fasta/Internal/Parser.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/Sequence/Parser/Fasta/Internal/Parser.hs
@@ -0,0 +1,36 @@
+module Bio.Sequence.Parser.Fasta.Internal.Parser
+  ( fastaParser
+  ) where
+
+import           Bio.Sequence     (Chain (..), Sequence)
+import           Data.Text        as T (Text, concat, pack, strip, unpack)
+import           Text.Parsec      (char, letter, many, many1, newline, noneOf,
+                                   spaces)
+import           Text.Parsec.Text (Parser)
+
+data FastaSequence = FastaSequence { sName    :: Text
+                                   , residues :: Text
+                                   } deriving (Show)
+
+fastaParser :: Parser [Sequence Char]
+fastaParser = (fastaSequenceToSequence <$>) <$> many fastaSequence
+
+fastaSequenceToSequence :: FastaSequence -> Sequence Char
+fastaSequenceToSequence fs = Chain { chainType = sName fs
+                                   , chainResidues = unpack (residues fs)
+                                   }
+
+fastaSequence :: Parser FastaSequence
+fastaSequence = FastaSequence <$> nameP <*> sequenceP
+
+nameP :: Parser Text
+nameP = strip <$> (T.pack <$> nameP')
+
+nameP' :: Parser String
+nameP' =  char '>' *> many (noneOf ['\n']) <* newline
+
+sequenceP :: Parser Text
+sequenceP = T.concat <$> many lineP
+
+lineP :: Parser Text
+lineP = T.pack <$> many1 letter <* spaces
diff --git a/test/Spec.hs b/test/Spec.hs
new file mode 100644
--- /dev/null
+++ b/test/Spec.hs
@@ -0,0 +1,63 @@
+{-# LANGUAGE OverloadedStrings #-}
+
+import           Test.Hspec
+
+import Data.Monoid ((<>))
+import Data.ByteString.Char8 (ByteString)
+
+import Bio.Sequence.Alignment
+import Bio.Sequence.Alignment.Matrix
+
+chains :: [ByteString]
+chains = [ "EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVA" <>
+           "RIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS"
+         , "EVQLVESGGGLVQPGGSLRLSCAASGFTFTDYTMDWVRQAPGKGLEWVA" <>
+           "DVNPNSGGSIYNQRFKGRFTLSVDRSKNTLYLQMNSLRAEDTAVYYCARNLGPSFYFDYWGQGTLVTVSS"
+         , "QVQLQQPGAELVKPGASVKMSCKASGYTFTSYNMHWVKQTPGRGLEWIG" <>
+           "AIYPGNGDTSYNQKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYYCARSTYYGGDWYFNVWGAGTTVTVSA"
+         , "EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSAI" <>
+           "TWNSGHIDYADSVEGRFTISRDNAKNSLYLQMNSLRAEDTAVYCAKVSYLSTASSLDYWGQGTLVTVSS"
+         , "EVQLVESGGGLVQPGGSLRLSCAASGYTFTNYGMNWVRQAPGKGLEWVG" <>
+           "WINTYTGEPTYAADFKRRFTFSLDTSKSTAYLQMNSLRAEDTAVYCAKYPHYYGSSHWYFDVWGQGTLVTVSS"
+         , "QVQLVQSGVEVKKPGASVKVSCKASGYTFTNYYMYWVRQAPGQGLEWMG" <>
+           "GINPSNGGTNFNEKFKNRVTLTTDSSTTTAYMELKSLQFDDTAVYYCARRDYRFDMGFDYWGQGTTVTVSS"
+         , "EVQLVESGGGLVQPGGSLRLSCAASGFTFSNYWMNWVRQAPGKGLEWVA" <>
+           "AINQDGSEKYYVGSVKGRFTISRDNAKNSLYLQMNSLRVEDTAVYYCVRDYYDILTDYYIHYWYFDLWGRGTLVTVSS"
+         ]
+
+combinations :: [Int]
+combinations = [fst $ alignment glob x y | x <- chains, y <- chains]
+  where glob = mkGlobal blosum62 (-5)
+
+results :: [Int]
+results = [ 645, 459, 345, 431, 401, 337, 405, 459, 634, 375, 437, 444
+          , 378, 425, 345, 375, 651, 306, 368, 418, 316, 431, 437, 306
+          , 628, 413, 312, 423, 401, 444, 368, 413, 669, 337, 436, 337
+          , 378, 418, 312, 337, 647, 304, 405, 425, 316, 423, 436, 304, 688]
+
+main :: IO ()
+main = hspec $ do
+         describe "Edit distance" $ do
+           it "align empty strings" $ do
+             let (_, (s', t')) = alignment mkEditDistance "" ""
+             s' `shouldBe` ""
+             t' `shouldBe` ""
+           it "align equal strings" $ do
+             let (_, (s', t')) = alignment mkEditDistance "AAA" "AAA"
+             s' `shouldBe` "AAA"
+             t' `shouldBe` "AAA"
+         describe "Semiglobal alignment" $ do
+           it "align without error" $ do
+             let s = "SVAPGQTARITCGEESLGSRSVIWYQQRPGQAPSLIIYNNNDRPSGIPDRFSGSPGSTFGTTATLTITSVEAGDEADYYCHIWDSRRPTNWVFGEGTTLIVL"
+             let t = "SSMSVSPGETAKISCGKESIGSRAVQWYQQKPGQPPSLIIYNNQDRPAGVPERFSASPDFRPGTTATLTITNVDAEDEADYYCHIYDARGGTNWVFDRGTTLTVL"
+             let (_, (s', _)) = alignment (mkSemiglobal blosum62 (-5)) s t
+             s' `shouldBe` "---SVAPGQTARITCGEESLGSRSVIWYQQRPGQAPSLIIYNNNDRPSGIPDRFSGSPGSTFGTTATLTITSVEAGDEADYYCHIWDSRRPTNWVFGEGTTLIVL"
+         describe "Global alignment" $ do
+           it "align antibodies" $ do
+             let (tra : per : _) = chains
+             let (score, (s', t')) = alignment (mkGlobal blosum62 (-5)) tra per
+             s' `shouldBe` "EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTY-IHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS"
+             t' `shouldBe` "EVQLVESGGGLVQPGGSLRLSCAASGFTFTD-YTMDWVRQAPGKGLEWVADVNPNSGGSIYNQRFKGRFTLSVDRSKNTLYLQMNSLRAEDTAVYYCARNLGPSFY-FDYWGQGTLVTVSS"
+             score `shouldBe` 459
+           it "align fast" $
+             combinations `shouldBe` results
diff --git a/test/SpecSimilarity.hs b/test/SpecSimilarity.hs
new file mode 100644
--- /dev/null
+++ b/test/SpecSimilarity.hs
@@ -0,0 +1,19 @@
+{-# LANGUAGE OverloadedStrings #-}
+
+import           Test.Hspec
+
+import           Data.ByteString.Char8          (ByteString)
+
+import           Bio.Sequence.Alignment.Scoring (similarity)
+
+main :: IO ()
+main = hspec $
+         describe "Similarity" $
+           it "simple strings" $ do
+             let sourceS = "QQYDLFIS" :: ByteString
+             let cdr31 = "KQSYDLPT" :: ByteString
+             let cdr32 = "QQYSDDPT" :: ByteString
+             let sim1 = similarity sourceS cdr31
+             let sim2 = similarity sourceS cdr32
+             sim1 `shouldBe` 0.44444442
+             sim2 `shouldBe` 0.44444442