diff --git a/bin/prepare_treebank.py b/bin/prepare_treebank.py
index 1de2dfdee..0d0e48921 100644
--- a/bin/prepare_treebank.py
+++ b/bin/prepare_treebank.py
@@ -60,15 +60,12 @@ def format_doc(section, filename, raw_paras, ptb_loc, dep_loc):
                     'brackets': []}
         for raw_sent in raw_sents:
             para['sents'].append(offset) 
-            _, brackets = read_ptb.parse(ptb_sents[i])
-            _, annot = read_conll.parse(dep_sents[i])
+            _, brackets = read_ptb.parse(ptb_sents[i], strip_bad_periods=True)
+            _, annot = read_conll.parse(dep_sents[i], strip_bad_periods=True)
             indices, word_idx, offset = _get_word_indices(raw_sent, 0, offset)
 
             for token in annot:
-                if token['head'] == -1:
-                    head = indices[token['id']]
-                else:
-                    head = indices[token['head']]
+                head = indices[token['head']]
                 try:
                     para['tokens'].append({'start': indices[token['id']],
                         'tag': token['tag'],
@@ -80,32 +77,34 @@ def format_doc(section, filename, raw_paras, ptb_loc, dep_loc):
                     print raw_sent
                     raise
             for label, start, end in brackets:
-                para['brackets'].append({'label': label,
-                    'start': indices[start],
-                    'end': indices[end-1]})
+                if start != end:
+                    para['brackets'].append({'label': label,
+                        'start': indices[start],
+                        'end': indices[end-1]})
             i += 1
         doc['paragraphs'].append(para)
     return doc
 
 
-def main(onto_dir, raw_dir, out_loc):
-    docs = []
+def main(onto_dir, raw_dir, out_dir):
     for i in range(25):
         section = str(i) if i >= 10 else ('0' + str(i))
         raw_loc = path.join(raw_dir, 'wsj%s.json' % section)
+        docs = []
         for j, raw_paras in enumerate(_iter_raw_files(raw_loc)):
             if section == '00':
                 j += 1
             filename = str(j) if j >= 9 else ('0' + str(j))
             if section == '04' and filename == '55':
                 continue
-            ptb_loc = path.join(onto_dir, section, 'wsj_%s%s.parse' % (section, filename))
-            dep_loc = ptb_loc + '.dep'
+            ptb_loc = path.join(onto_dir, section, 'wsj_%s%s.mrg' % (section, filename))
+            dep_loc = ptb_loc + '.3.pa.gs.tab'
             if path.exists(ptb_loc) and path.exists(dep_loc):
                 print ptb_loc
                 doc = format_doc(section, filename, raw_paras, ptb_loc, dep_loc)
                 docs.append(doc)
-    json.dump(docs, open(out_loc, 'w'))
+        with open(path.join(out_dir, '%s.json' % section), 'w') as file_:
+            json.dump(docs, file_)
 
 
 if __name__ == '__main__':
diff --git a/spacy/munge/__init__.py b/spacy/munge/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/spacy/munge/align_raw.py b/spacy/munge/align_raw.py
new file mode 100644
index 000000000..5d3954b11
--- /dev/null
+++ b/spacy/munge/align_raw.py
@@ -0,0 +1,175 @@
+"""Align the raw sentences from Read et al (2012) to the PTB tokenization,
+outputing the format:
+
+[{
+    section: int,
+    file: string,
+    paragraphs: [{
+        raw: string,
+        segmented: string,
+        tokens: [int]}]}]
+"""
+import plac
+from pathlib import Path
+import json
+from os import path
+
+from spacy.munge import read_ptb
+
+
+def read_unsegmented(section_loc):
+    # Arbitrary patches applied to the _raw_ text to promote alignment.
+    patches = (
+        ('. . . .', '...'),
+        ('....', '...'),
+        ('Co..', 'Co.'),
+        ("`", "'"),
+    )
+    
+    paragraphs = []
+    with open(section_loc) as file_:
+        para = []
+        for line in file_:
+            if line.startswith('['):
+                line = line.split('|', 1)[1].strip()
+                for find, replace in patches:
+                    line = line.replace(find, replace)
+                para.append(line)
+            else:
+                paragraphs.append(para)
+                para = []
+        paragraphs.append(para)
+    return paragraphs
+
+
+def read_ptb_sec(ptb_sec_dir):
+    ptb_sec_dir = Path(ptb_sec_dir)
+    files = []
+    for loc in ptb_sec_dir.iterdir():
+        if not str(loc).endswith('parse') and not str(loc).endswith('mrg'):
+            continue
+        with loc.open() as file_:
+            text = file_.read()
+        sents = []
+        for parse_str in read_ptb.split(text):
+            words, brackets = read_ptb.parse(parse_str, strip_bad_periods=True)
+            words = [_reform_ptb_word(word) for word in words]
+            string = ' '.join(words)
+            sents.append(string)
+        files.append(sents)
+    return files
+
+
+def _reform_ptb_word(tok):
+    tok = tok.replace("``", '"')
+    tok = tok.replace("`", "'")
+    tok = tok.replace("''", '"')
+    tok = tok.replace('\\', '')
+    tok = tok.replace('-LCB-', '{')
+    tok = tok.replace('-RCB-', '}')
+    tok = tok.replace('-RRB-', ')')
+    tok = tok.replace('-LRB-', '(')
+    tok = tok.replace("'T-", "'T")
+    return tok
+ 
+
+def get_alignment(raw_by_para, ptb_by_file):
+    # These are list-of-lists, by paragraph and file respectively.
+    # Flatten them into a list of (outer_id, inner_id, item) triples
+    raw_sents = _flatten(raw_by_para)
+    ptb_sents = _flatten(ptb_by_file)
+
+    assert len(raw_sents) == len(ptb_sents)
+
+    output = []
+    for (p_id, p_sent_id, raw), (f_id, f_sent_id, ptb) in zip(raw_sents, ptb_sents):
+        alignment = align_chars(raw, ptb)
+        sepped = []
+        for i, c in enumerate(ptb):
+            if alignment[i] is False:
+                sepped.append('<SEP>')
+            else:
+                sepped.append(c)
+        output.append((f_id, p_id, f_sent_id, ''.join(sepped)))
+    return output
+
+
+def _flatten(nested):
+    flat = []
+    for id1, inner in enumerate(nested):
+        flat.extend((id1, id2, item) for id2, item in enumerate(inner))
+    return flat
+
+
+def align_chars(raw, ptb):
+    i = 0
+    j = 0
+
+    length = len(raw)
+    alignment = [False for _ in range(len(ptb))]
+    while i < length:
+        if raw[i] == ' ' and ptb[j] == ' ':
+            alignment[j] = True
+            i += 1
+            j += 1
+        elif raw[i] == ' ':
+            i += 1
+        elif ptb[j] == ' ':
+            j += 1
+        assert raw[i].lower() == ptb[j].lower(), raw[i:1]
+        alignment[j] = i
+        i += 1; j += 1
+    return alignment
+
+
+def group_into_files(sents):
+    last_id = 0
+    this = []
+    output = []
+    for f_id, p_id, s_id, sent in sents:
+        if f_id != last_id:
+            output.append(this)
+            this = []
+        this.append((f_id, p_id, s_id, sent))
+        last_id = f_id
+    if this:
+        output.append(this)
+    return output
+
+
+def group_into_paras(sents):
+    last_id = 0
+    this = []
+    output = []
+    for f_id, p_id, s_id, sent in sents:
+        if p_id != last_id and this:
+            output.append(this)
+            this = []
+        this.append((sent))
+        last_id = p_id
+    if this:
+        output.append(this)
+    return output
+
+
+def get_sections(odc_dir, ptb_dir, out_dir):
+    for i in range(25):
+        section = str(i) if i >= 10 else ('0' + str(i))
+        odc_loc = path.join(odc_dir, 'wsj%s.txt' % section)
+        ptb_sec = path.join(ptb_dir, section)
+        out_loc = path.join(out_dir, 'wsj%s.json' % section)
+        yield odc_loc, ptb_sec, out_loc
+
+
+def main(odc_dir, ptb_dir, out_dir):
+    for odc_loc, ptb_sec_dir, out_loc in get_sections(odc_dir, ptb_dir, out_dir):
+        raw_paragraphs = read_unsegmented(odc_loc)
+        ptb_files = read_ptb_sec(ptb_sec_dir)
+        aligned = get_alignment(raw_paragraphs, ptb_files)
+        files = [group_into_paras(f) for f in group_into_files(aligned)]
+        with open(out_loc, 'w') as file_:
+            json.dump(files, file_)
+
+
+if __name__ == '__main__':
+    plac.call(main)
diff --git a/spacy/munge/read_conll.py b/spacy/munge/read_conll.py
new file mode 100644
index 000000000..6b563c1b7
--- /dev/null
+++ b/spacy/munge/read_conll.py
@@ -0,0 +1,40 @@
+from __future__ import unicode_literals
+
+
+def split(text):
+    return [sent.strip() for sent in text.split('\n\n') if sent.strip()]
+
+
+def parse(sent_text, strip_bad_periods=False):
+    sent_text = sent_text.strip()
+    assert sent_text
+    annot = []
+    words = []
+    i = 0
+    for line in sent_text.split('\n'):
+        word, tag, head, dep = line.split()
+        if strip_bad_periods and words and _is_bad_period(words[-1], word):
+            continue
+  
+        annot.append({
+            'id': i,
+            'word': word,
+            'tag': tag,
+            'head': int(head) - 1 if int(head) != 0 else i,
+            'dep': dep})
+        words.append(word)
+        i += 1
+    return words, annot
+
+
+def _is_bad_period(prev, period):
+    if period != '.':
+        return False
+    elif prev == '.':
+        return False
+    elif not prev.endswith('.'):
+        return False
+    else:
+        return True
+
+
diff --git a/spacy/munge/read_ptb.py b/spacy/munge/read_ptb.py
new file mode 100644
index 000000000..609397ba0
--- /dev/null
+++ b/spacy/munge/read_ptb.py
@@ -0,0 +1,65 @@
+import re
+import os
+from os import path
+
+
+def parse(sent_text, strip_bad_periods=False):
+    sent_text = sent_text.strip()
+    assert sent_text and sent_text.startswith('(')
+    open_brackets = []
+    brackets = []
+    bracketsRE = re.compile(r'(\()([^\s\)\(]+)|([^\s\)\(]+)?(\))')
+    word_i = 0
+    words = []
+    # Remove outermost bracket
+    if sent_text.startswith('(('):
+        sent_text = sent_text.replace('((', '( (', 1)
+    for match in bracketsRE.finditer(sent_text[2:-1]):
+        open_, label, text, close = match.groups()
+        if open_:
+            assert not close
+            assert label.strip()
+            open_brackets.append((label, word_i))
+        else:
+            assert close
+            label, start = open_brackets.pop()
+            assert label.strip()
+            if strip_bad_periods and words and _is_bad_period(words[-1], text):
+                continue
+            # Traces leave 0-width bracket, but no token
+            if text and label != '-NONE-':
+                words.append(text)
+                word_i += 1
+            else:
+                brackets.append((label, start, word_i))
+    return words, brackets
+
+
+def _is_bad_period(prev, period):
+    if period != '.':
+        return False
+    elif prev == '.':
+        return False
+    elif not prev.endswith('.'):
+        return False
+    else:
+        return True
+
+
+def split(text):
+    sentences = []
+    current = []
+
+    for line in text.strip().split('\n'):
+        line = line.rstrip()
+        if not line:
+            continue
+        # Detect the start of sentences by line starting with (
+        # This is messy, but it keeps bracket parsing at the sentence level
+        if line.startswith('(') and current:
+            sentences.append('\n'.join(current))
+            current = []
+        current.append(line)
+    if current:
+        sentences.append('\n'.join(current))
+    return sentences