nltk 3.2__zip → 3.3__zip

nltk-3.3/nltk/metrics/aline.py

@@ -0,0 +1,607 @@
+# -*- coding: utf-8 -*-
+# Natural Language Toolkit: ALINE
+#
+# Copyright (C) 2001-2018 NLTK Project
+# Author: Greg Kondrak <gkondrak@ualberta.ca>
+#         Geoff Bacon <bacon@berkeley.edu> (Python port)
+# URL: <http://nltk.org/>
+# For license information, see LICENSE.TXT
+
+"""
+ALINE
+http://webdocs.cs.ualberta.ca/~kondrak/
+Copyright 2002 by Grzegorz Kondrak.
+
+ALINE is an algorithm for aligning phonetic sequences, described in [1].
+This module is a port of Kondrak's (2002) ALINE. It provides functions for
+phonetic sequence alignment and similarity analysis. These are useful in
+historical linguistics, sociolinguistics and synchronic phonology.
+
+ALINE has parameters that can be tuned for desired output. These parameters are:
+- C_skip, C_sub, C_exp, C_vwl
+- Salience weights
+- Segmental features
+
+In this implementation, some parameters have been changed from their default
+values as described in [1], in order to replicate published results. All changes
+are noted in comments.
+
+Example usage
+-------------
+
+# Get optimal alignment of two phonetic sequences
+
+>>> align('θin', 'tenwis') # doctest: +SKIP
+[[('θ', 't'), ('i', 'e'), ('n', 'n'), ('-', 'w'), ('-', 'i'), ('-', 's')]]
+
+[1] G. Kondrak. Algorithms for Language Reconstruction. PhD dissertation,
+University of Toronto.
+"""
+
+from __future__ import unicode_literals
+
+try:
+    import numpy as np
+except ImportError:
+    np = None
+
+# === Constants ===
+
+inf = float('inf')
+
+# Default values for maximum similarity scores (Kondrak 2002: 54)
+C_skip = 10 # Indels
+C_sub  = 35  # Substitutions
+C_exp  = 45  # Expansions/compressions
+C_vwl  = 5  # Vowel/consonant relative weight (decreased from 10)
+
+consonants = ['B', 'N', 'R', 'b', 'c', 'd', 'f', 'g', 'h', 'j', 'k', 'l', 'm',
+              'n', 'p', 'q', 'r', 's', 't', 'v', 'x', 'z', 'ç', 'ð', 'ħ',
+              'ŋ', 'ɖ', 'ɟ', 'ɢ', 'ɣ', 'ɦ', 'ɬ', 'ɮ', 'ɰ', 'ɱ', 'ɲ', 'ɳ', 'ɴ',
+              'ɸ', 'ɹ', 'ɻ', 'ɽ', 'ɾ', 'ʀ', 'ʁ', 'ʂ', 'ʃ', 'ʈ', 'ʋ', 'ʐ ', 'ʒ',
+              'ʔ', 'ʕ', 'ʙ', 'ʝ', 'β', 'θ', 'χ', 'ʐ', 'w']
+
+# Relevant features for comparing consonants and vowels
+R_c = ['aspirated', 'lateral', 'manner', 'nasal', 'place', 'retroflex',
+       'syllabic', 'voice']
+# 'high' taken out of R_v because same as manner
+R_v = ['back', 'lateral', 'long', 'manner', 'nasal', 'place',
+       'retroflex', 'round', 'syllabic', 'voice']
+
+# Flattened feature matrix (Kondrak 2002: 56)
+similarity_matrix = {
+   #place
+   'bilabial': 1.0, 'labiodental': 0.95, 'dental': 0.9,
+   'alveolar': 0.85, 'retroflex': 0.8, 'palato-alveolar': 0.75,
+   'palatal': 0.7, 'velar': 0.6, 'uvular': 0.5, 'pharyngeal': 0.3,
+   'glottal': 0.1, 'labiovelar': 1.0, 'vowel': -1.0, # added 'vowel'
+   #manner
+   'stop': 1.0, 'affricate': 0.9, 'fricative': 0.85, # increased fricative from 0.8
+   'trill': 0.7, 'tap': 0.65, 'approximant': 0.6, 'high vowel': 0.4,
+   'mid vowel': 0.2, 'low vowel': 0.0, 'vowel2': 0.5, # added vowel
+   #high
+   'high': 1.0, 'mid': 0.5, 'low': 0.0,
+   #back
+   'front': 1.0, 'central': 0.5, 'back': 0.0,
+   #binary features
+   'plus': 1.0, 'minus': 0.0
+}
+
+# Relative weights of phonetic features (Kondrak 2002: 55)
+salience = {
+   'syllabic': 5,
+   'place': 40,
+   'manner': 50,
+   'voice': 5, # decreased from 10
+   'nasal': 20, # increased from 10
+   'retroflex': 10,
+   'lateral': 10,
+   'aspirated': 5,
+   'long': 0, # decreased from 1
+   'high': 3, # decreased from 5
+   'back': 2, # decreased from 5
+   'round': 2 # decreased from 5
+}
+
+# (Kondrak 2002: 59-60)
+feature_matrix = {
+# Consonants
+'p': {'place': 'bilabial', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'b': {'place': 'bilabial', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'t': {'place': 'alveolar', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'d': {'place': 'alveolar', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ʈ': {'place': 'retroflex', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'plus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɖ': {'place': 'retroflex', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'plus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'c': {'place': 'palatal', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɟ': {'place': 'palatal', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'k': {'place': 'velar', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'g': {'place': 'velar', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'q': {'place': 'uvular', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɢ': {'place': 'uvular', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ʔ': {'place': 'glottal', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'m': {'place': 'bilabial', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'plus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɱ': {'place': 'labiodental', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'plus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'n': {'place': 'alveolar', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'plus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɳ': {'place': 'retroflex', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'plus', 'retroflex': 'plus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɲ': {'place': 'palatal', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'plus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ŋ': {'place': 'velar', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'plus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɴ': {'place': 'uvular', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'plus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'N': {'place': 'uvular', 'manner': 'stop', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'plus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ʙ': {'place': 'bilabial', 'manner': 'trill', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'B': {'place': 'bilabial', 'manner': 'trill', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'r': {'place': 'alveolar', 'manner': 'trill', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'plus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ʀ': {'place': 'uvular', 'manner': 'trill', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'R': {'place': 'uvular', 'manner': 'trill', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɾ': {'place': 'alveolar', 'manner': 'tap', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɽ': {'place': 'retroflex', 'manner': 'tap', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'plus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɸ': {'place': 'bilabial', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'β': {'place': 'bilabial', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'f': {'place': 'labiodental', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'v': {'place': 'labiodental', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'θ': {'place': 'dental', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ð': {'place': 'dental', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'s': {'place': 'alveolar', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'z': {'place': 'alveolar', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ʃ': {'place': 'palato-alveolar', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ʒ': {'place': 'palato-alveolar', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ʂ': {'place': 'retroflex', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'plus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ʐ': {'place': 'retroflex', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'plus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ç': {'place': 'palatal', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ʝ': {'place': 'palatal', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'x': {'place': 'velar', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɣ': {'place': 'velar', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'χ': {'place': 'uvular', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ʁ': {'place': 'uvular', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ħ': {'place': 'pharyngeal', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ʕ': {'place': 'pharyngeal', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'h': {'place': 'glottal', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɦ': {'place': 'glottal', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɬ': {'place': 'alveolar', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'minus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'plus', 'aspirated': 'minus'},
+
+'ɮ': {'place': 'alveolar', 'manner': 'fricative', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'plus', 'aspirated': 'minus'},
+
+'ʋ': {'place': 'labiodental', 'manner': 'approximant', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɹ': {'place': 'alveolar', 'manner': 'approximant', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɻ': {'place': 'retroflex', 'manner': 'approximant', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'plus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'j': {'place': 'palatal', 'manner': 'approximant', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'ɰ': {'place': 'velar', 'manner': 'approximant', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+'l': {'place': 'alveolar', 'manner': 'approximant', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'plus', 'aspirated': 'minus'},
+
+'w': {'place': 'labiovelar', 'manner': 'approximant', 'syllabic': 'minus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'aspirated': 'minus'},
+
+# Vowels
+
+'i': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'high',
+'back': 'front','round': 'minus', 'long': 'minus', 'aspirated': 'minus'},
+
+'y': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'high',
+'back': 'front','round': 'plus', 'long': 'minus', 'aspirated': 'minus'},
+
+'e': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'mid',
+'back': 'front','round': 'minus', 'long': 'minus', 'aspirated': 'minus'},
+
+'E': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'mid',
+'back': 'front','round': 'minus', 'long': 'plus', 'aspirated': 'minus'},
+
+'ø': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'mid',
+'back': 'front','round': 'plus', 'long': 'minus', 'aspirated': 'minus'},
+
+'ɛ': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'mid',
+'back': 'front','round': 'minus', 'long': 'minus', 'aspirated': 'minus'},
+
+'œ': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'mid',
+'back': 'front','round': 'plus', 'long': 'minus', 'aspirated': 'minus'},
+
+'æ': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'low',
+'back': 'front','round': 'minus', 'long': 'minus', 'aspirated': 'minus'},
+
+'a': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'low',
+'back': 'front','round': 'minus', 'long': 'minus', 'aspirated': 'minus'},
+
+'A': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'low',
+'back': 'front','round': 'minus', 'long': 'plus', 'aspirated': 'minus'},
+
+'ɨ': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'high',
+'back': 'central','round': 'minus', 'long': 'minus', 'aspirated': 'minus'},
+
+'ʉ': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'high',
+'back': 'central','round': 'plus', 'long': 'minus', 'aspirated': 'minus'},
+
+'ə': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'mid',
+'back': 'central','round': 'minus', 'long': 'minus', 'aspirated': 'minus'},
+
+'u': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'high',
+'back': 'back','round': 'plus', 'long': 'minus', 'aspirated': 'minus'},
+
+'U': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'high',
+'back': 'back','round': 'plus', 'long': 'plus', 'aspirated': 'minus'},
+
+'o': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'mid',
+'back': 'back','round': 'plus', 'long': 'minus', 'aspirated': 'minus'},
+
+'O': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'mid',
+'back': 'back','round': 'plus', 'long': 'plus', 'aspirated': 'minus'},
+
+'ɔ': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'mid',
+'back': 'back','round': 'plus', 'long': 'minus', 'aspirated': 'minus'},
+
+'ɒ': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'low',
+'back': 'back','round': 'minus', 'long': 'minus', 'aspirated': 'minus'},
+
+'I': {'place': 'vowel', 'manner': 'vowel2', 'syllabic': 'plus', 'voice': 'plus',
+'nasal': 'minus', 'retroflex': 'minus', 'lateral': 'minus', 'high': 'high',
+'back': 'front','round': 'minus', 'long': 'plus', 'aspirated': 'minus'},
+
+}
+
+# === Algorithm ===
+
+def align(str1, str2, epsilon=0):
+    """
+    Compute the alignment of two phonetic strings.
+
+    :type str1, str2: str
+    :param str1, str2: Two strings to be aligned
+    :type epsilon: float (0.0 to 1.0)
+    :param epsilon: Adjusts threshold similarity score for near-optimal alignments
+
+    :rtpye: list(list(tuple(str, str)))
+    :return: Alignment(s) of str1 and str2
+
+    (Kondrak 2002: 51)
+    """
+    if np == None:
+      raise ImportError('You need numpy in order to use the align function')
+
+    assert 0.0 <= epsilon <= 1.0, "Epsilon must be between 0.0 and 1.0."
+    m = len(str1)
+    n = len(str2)
+    # This includes Kondrak's initialization of row 0 and column 0 to all 0s.
+    S = np.zeros((m+1, n+1), dtype=float)
+
+    # If i <= 1 or j <= 1, don't allow expansions as it doesn't make sense,
+    # and breaks array and string indices. Make sure they never get chosen
+    # by setting them to -inf.
+    for i in range(1, m+1):
+        for j in range(1, n+1):
+            edit1 = S[i-1, j] + sigma_skip(str1[i-1])
+            edit2 = S[i, j-1] + sigma_skip(str2[j-1])
+            edit3 = S[i-1, j-1] + sigma_sub(str1[i-1], str2[j-1])
+            if i > 1:
+                edit4 = S[i-2, j-1] + sigma_exp(str2[j-1], str1[i-2:i])
+            else:
+                edit4 = -inf
+            if j > 1:
+                edit5 = S[i-1, j-2] + sigma_exp(str1[i-1], str2[j-2:j])
+            else:
+                edit5 = -inf
+            S[i, j] = max(edit1, edit2, edit3, edit4, edit5, 0)
+
+    T = (1-epsilon)*np.amax(S) # Threshold score for near-optimal alignments
+
+    alignments = []
+    for i in range(1, m+1):
+        for j in range(1, n+1):
+            if S[i,j] >= T:
+                alignments.append(_retrieve(i, j, 0, S, T, str1, str2, []))
+    return alignments
+
+def _retrieve(i, j, s, S, T, str1, str2, out):
+    """
+    Retrieve the path through the similarity matrix S starting at (i, j).
+
+    :rtype: list(tuple(str, str))
+    :return: Alignment of str1 and str2
+    """
+    if S[i, j] == 0:
+        return out
+    else:
+        if j > 1 and S[i-1, j-2] + sigma_exp(str1[i-1], str2[j-2:j]) + s >= T:
+            out.insert(0, (str1[i-1], str2[j-2:j]))
+            _retrieve(i-1, j-2, s+sigma_exp(str1[i-1], str2[j-2:j]), S, T, str1, str2, out)
+        elif i > 1 and S[i-2, j-1] + sigma_exp(str2[j-1], str1[i-2:i]) + s >= T:
+            out.insert(0, (str1[i-2:i], str2[j-1]))
+            _retrieve(i-2, j-1, s+sigma_exp(str2[j-1], str1[i-2:i]), S, T, str1, str2, out)
+        elif S[i, j-1] + sigma_skip(str2[j-1]) + s >= T:
+            out.insert(0, ('-', str2[j-1]))
+            _retrieve(i, j-1, s+sigma_skip(str2[j-1]), S, T, str1, str2, out)
+        elif S[i-1, j] + sigma_skip(str1[i-1]) + s >= T:
+            out.insert(0, (str1[i-1], '-'))
+            _retrieve(i-1, j, s+sigma_skip(str1[i-1]), S, T, str1, str2, out)
+        elif S[i-1, j-1] + sigma_sub(str1[i-1], str2[j-1]) + s >= T:
+            out.insert(0, (str1[i-1], str2[j-1]))
+            _retrieve(i-1, j-1, s+sigma_sub(str1[i-1], str2[j-1]), S, T, str1, str2, out)
+    return out
+
+def sigma_skip(p):
+    """
+    Returns score of an indel of P.
+
+    (Kondrak 2002: 54)
+    """
+    return C_skip
+
+def sigma_sub(p, q):
+    """
+    Returns score of a substitution of P with Q.
+
+    (Kondrak 2002: 54)
+    """
+    return C_sub - delta(p, q) - V(p) - V(q)
+
+def sigma_exp(p, q):
+    """
+    Returns score of an expansion/compression.
+
+    (Kondrak 2002: 54)
+    """
+    q1 = q[0]
+    q2 = q[1]
+    return C_exp - delta(p, q1) - delta(p, q2) - V(p) - max(V(q1), V(q2))
+
+def delta(p, q):
+    """
+    Return weighted sum of difference between P and Q.
+
+    (Kondrak 2002: 54)
+    """
+    features = R(p, q)
+    total = 0
+    for f in features:
+        total += diff(p, q, f) * salience[f]
+    return total
+
+def diff(p, q, f):
+    """
+    Returns difference between phonetic segments P and Q for feature F.
+
+    (Kondrak 2002: 52, 54)
+    """
+    p_features, q_features = feature_matrix[p], feature_matrix[q]
+    return abs(similarity_matrix[p_features[f]] - similarity_matrix[q_features[f]])
+
+def R(p, q):
+    """
+    Return relevant features for segment comparsion.
+
+    (Kondrak 2002: 54)
+    """
+    if p in consonants or q in consonants:
+        return R_c
+    return R_v
+
+def V(p):
+    """
+    Return vowel weight if P is vowel.
+
+    (Kondrak 2002: 54)
+    """
+    if p in consonants:
+        return 0
+    return C_vwl
+
+# === Test ===
+
+def demo():
+    """
+    A demonstration of the result of aligning phonetic sequences
+    used in Kondrak's (2002) dissertation.
+    """
+    data = [pair.split(',') for pair in cognate_data.split('\n')]
+    for pair in data:
+        alignment = align(pair[0], pair[1])[0]
+        alignment = ['({}, {})'.format(a[0], a[1]) for a in alignment]
+        alignment = ' '.join(alignment)
+        print('{} ~ {} : {}'.format(pair[0], pair[1], alignment))
+
+cognate_data = """jo,ʒə
+tu,ty
+nosotros,nu
+kjen,ki
+ke,kwa
+todos,tu
+una,ən
+dos,dø
+tres,trwa
+ombre,om
+arbol,arbrə
+pluma,plym
+kabeθa,kap
+boka,buʃ
+pje,pje
+koraθon,kœr
+ber,vwar
+benir,vənir
+deθir,dir
+pobre,povrə
+ðis,dIzes
+ðæt,das
+wat,vas
+nat,nixt
+loŋ,laŋ
+mæn,man
+fleʃ,flajʃ
+bləd,blyt
+feðər,fEdər
+hær,hAr
+ir,Or
+aj,awgə
+nowz,nAzə
+mawθ,munt
+təŋ,tsuŋə
+fut,fys
+nij,knI
+hænd,hant
+hart,herts
+livər,lEbər
+ænd,ante
+æt,ad
+blow,flAre
+ir,awris
+ijt,edere
+fiʃ,piʃkis
+flow,fluere
+staɾ,stella
+ful,plenus
+græs,gramen
+hart,kordis
+horn,korny
+aj,ego
+nij,genU
+məðər,mAter
+mawntən,mons
+nejm,nomen
+njuw,nowus
+wən,unus
+rawnd,rotundus
+sow,suere
+sit,sedere
+θrij,tres
+tuwθ,dentis
+θin,tenwis
+kinwawa,kenuaʔ
+nina,nenah
+napewa,napɛw
+wapimini,wapemen
+namesa,namɛʔs
+okimawa,okemaw
+ʃiʃipa,seʔsep
+ahkohkwa,ahkɛh
+pematesiweni,pematesewen
+asenja,aʔsɛn"""
+
+if __name__ == '__main__':
+    demo()