diff --git a/lib/create_adaptive_distinguishing_sequence.cpp b/lib/adaptive_distinguishing_sequence.cpp
similarity index 70%
rename from lib/create_adaptive_distinguishing_sequence.cpp
rename to lib/adaptive_distinguishing_sequence.cpp
index 4aebc3b..7d281b4 100644
--- a/lib/create_adaptive_distinguishing_sequence.cpp
+++ b/lib/adaptive_distinguishing_sequence.cpp
@@ -1,5 +1,4 @@
-#include "create_adaptive_distinguishing_sequence.hpp"
-#include "create_splitting_tree.hpp"
+#include "adaptive_distinguishing_sequence.hpp"
 
 #include <algorithm>
 #include <cassert>
@@ -8,18 +7,26 @@
 
 using namespace std;
 
-distinguishing_sequence create_adaptive_distinguishing_sequence(const result & splitting_tree){
+adaptive_distinguishing_sequence::adaptive_distinguishing_sequence(size_t N, size_t depth)
+: CI(N)
+, depth(depth)
+{
+	for(size_t i = 0; i < N; ++i)
+		CI[i] = {i, i};
+}
+
+adaptive_distinguishing_sequence create_adaptive_distinguishing_sequence(const result & splitting_tree){
 	const auto & root = splitting_tree.root;
 	const auto & succession = splitting_tree.successor_cache;
 	const auto N = root.states.size();
 
-	distinguishing_sequence sequence(N, 0);
+	adaptive_distinguishing_sequence sequence(N, 0);
 
-	queue<reference_wrapper<distinguishing_sequence>> work;
+	queue<reference_wrapper<adaptive_distinguishing_sequence>> work;
 	work.push(sequence);
 
 	while(!work.empty()){
-		distinguishing_sequence & node = work.front();
+		adaptive_distinguishing_sequence & node = work.front();
 		work.pop();
 
 		if(node.CI.size() < 2) continue;
@@ -37,7 +44,7 @@ distinguishing_sequence create_adaptive_distinguishing_sequence(const result & s
 
 		node.word = oboom.seperator;
 		for(auto && c : oboom.children){
-			distinguishing_sequence new_c(0, node.depth + 1);
+			adaptive_distinguishing_sequence new_c(0, node.depth + 1);
 
 			size_t i = 0;
 			size_t j = 0;
diff --git a/lib/adaptive_distinguishing_sequence.hpp b/lib/adaptive_distinguishing_sequence.hpp
new file mode 100644
index 0000000..8f0a942
--- /dev/null
+++ b/lib/adaptive_distinguishing_sequence.hpp
@@ -0,0 +1,25 @@
+#pragma once
+
+#include "types.hpp"
+#include "splitting_tree.hpp"
+
+#include <utility>
+
+/*
+ * The adaptive distinguishing sequence as described in Lee & Yannakakis. This
+ * is not a sequence, but a decision tree! It can be constructed from the Lee
+ * & Yannakakis-style splitting tree. We also need some other data produced
+ * by the splitting tree algorithm.
+ */
+
+struct adaptive_distinguishing_sequence {
+	adaptive_distinguishing_sequence(size_t N, size_t depth);
+
+	// current, initial
+	std::vector<std::pair<state, state>> CI;
+	std::vector<adaptive_distinguishing_sequence> children;
+	word word;
+	size_t depth;
+};
+
+adaptive_distinguishing_sequence create_adaptive_distinguishing_sequence(result const & splitting_tree);
diff --git a/lib/create_adaptive_distinguishing_sequence.hpp b/lib/create_adaptive_distinguishing_sequence.hpp
deleted file mode 100644
index ee60740..0000000
--- a/lib/create_adaptive_distinguishing_sequence.hpp
+++ /dev/null
@@ -1,32 +0,0 @@
-#pragma once
-
-#include "mealy.hpp"
-
-#include <vector>
-#include <utility>
-
-struct result;
-struct distinguishing_sequence;
-
-
-// Creates a distinguishing sequence based on the output of the first algorithm
-distinguishing_sequence create_adaptive_distinguishing_sequence(result const & splitting_tree);
-
-
-// The adaptive distinguishing sequence as described in Lee & Yannakakis
-// This is really a tree!
-struct distinguishing_sequence {
-	distinguishing_sequence(size_t N, size_t depth)
-	: CI(N)
-	, depth(depth)
-	{
-		for(size_t i = 0; i < N; ++i)
-			CI[i] = {i, i};
-	}
-
-	// current, initial
-	std::vector<std::pair<state, state>> CI;
-	std::vector<input> word;
-	std::vector<distinguishing_sequence> children;
-	size_t depth;
-};
diff --git a/lib/create_splitting_tree.hpp b/lib/create_splitting_tree.hpp
deleted file mode 100644
index 782324b..0000000
--- a/lib/create_splitting_tree.hpp
+++ /dev/null
@@ -1,44 +0,0 @@
-#pragma once
-
-#include "mealy.hpp"
-#include "splitting_tree.hpp"
-
-#include <vector>
-
-struct options;
-struct result;
-
-
-// Creates a Lee & Yannakakis style splitting tree
-// Depending on the options it can also create the classical Hopcroft splitting tree
-result create_splitting_tree(Mealy const & m, options opt);
-
-
-// The algorithm can be altered in some ways. This struct provides options
-// to the algorithm
-struct options {
-	bool check_validity = true;
-};
-
-constexpr options with_validity_check{true};
-constexpr options without_validity_check{false};
-
-
-// The algorithm constructs more than the splitting tree
-// We capture the other information as well
-struct result {
-	result(size_t N)
-	: root(N, 0)
-	, successor_cache()
-	, is_complete(true)
-	{}
-
-	// The splitting tree as described in Lee & Yannakakis
-	splijtboom root;
-
-	// Encodes f_u : depth -> state -> state, where only the depth of u is of importance
-	std::vector<std::vector<state>> successor_cache;
-
-	// false <-> no adaptive distinguishing sequence
-	bool is_complete;
-};
diff --git a/lib/io.hpp b/lib/io.hpp
new file mode 100644
index 0000000..c25f3c7
--- /dev/null
+++ b/lib/io.hpp
@@ -0,0 +1,31 @@
+#pragma once
+
+#include "phantom.hpp"
+#include "mealy.hpp"
+
+#include <boost/iostreams/device/file_descriptor.hpp>
+#include <boost/iostreams/filter/gzip.hpp>
+#include <boost/iostreams/filtering_stream.hpp>
+
+#include <boost/serialization/serialization.hpp>
+#include <boost/serialization/string.hpp>
+#include <boost/serialization/vector.hpp>
+
+#include <boost/archive/text_oarchive.hpp>
+#include <boost/archive/text_iarchive.hpp>
+#include <boost/archive/binary_oarchive.hpp>
+#include <boost/archive/binary_iarchive.hpp>
+
+#include <iostream>
+#include <fstream>
+
+namespace boost {
+namespace serialization {
+
+template<class Archive, typename B, typename T>
+void serialize(Archive & ar, phantom<B, T> & value, const unsigned int /*version*/){
+	ar & value.x;
+}
+
+} // namespace serialization
+} // namespace boost
diff --git a/lib/mealy.hpp b/lib/mealy.hpp
index e47cbf0..80cd396 100644
--- a/lib/mealy.hpp
+++ b/lib/mealy.hpp
@@ -1,18 +1,11 @@
 #pragma once
 
-#include "phantom.hpp"
+#include "types.hpp"
 
 #include <map>
 #include <string>
 #include <vector>
 
-/* We use size_t's for easy indexing. But we do not want to mix states and
- * inputs. We use phantom typing to "generate" distinguished types :).
- */
-using state = phantom<size_t, struct state_tag>;
-using input = phantom<size_t, struct input_tag>;
-using output = phantom<size_t, struct output_tag>;
-
 /*
  * Structure used for reading mealy files from dot files.
  * Everything is indexed by size_t's, so that we can index vectors
@@ -20,7 +13,7 @@ using output = phantom<size_t, struct output_tag>;
  * to these size_t's. Can only represent deterministic machines,
  * but partiality still can occur.
  */
-struct Mealy {
+struct mealy {
 	struct edge {
 		state to = -1;
 		output output = -1;
@@ -39,7 +32,7 @@ struct Mealy {
 	size_t output_size = 0;
 };
 
-inline auto is_complete(const Mealy & m){
+inline auto is_complete(const mealy & m){
 	for(state n = 0; n < m.graph_size; ++n){
 		if(m.graph[n.base()].size() != m.input_size) return false;
 		for(auto && e : m.graph[n.base()]) if(e.to == -1 || e.output == -1) return false;
@@ -47,13 +40,13 @@ inline auto is_complete(const Mealy & m){
 	return true;
 }
 
-inline auto apply(Mealy const & m, state state, input input){
+inline auto apply(mealy const & m, state state, input input){
 	return m.graph[state.base()][input.base()];
 }
 
 template <typename Iterator>
-auto apply(Mealy const & m, state state, Iterator b, Iterator e){
-	Mealy::edge ret;
+auto apply(mealy const & m, state state, Iterator b, Iterator e){
+	mealy::edge ret;
 	while(b != e){
 		ret = apply(m, state, *b++);
 		state = ret.to;
diff --git a/lib/phantom.hpp b/lib/phantom.hpp
index 07687b5..39e53ce 100644
--- a/lib/phantom.hpp
+++ b/lib/phantom.hpp
@@ -1,6 +1,7 @@
 #pragma once
 
 #include <boost/operators.hpp>
+
 #include <iosfwd>
 
 template <typename Base, typename T>
diff --git a/lib/read_mealy_from_dot.cpp b/lib/read_mealy_from_dot.cpp
index 3124c67..0a44850 100644
--- a/lib/read_mealy_from_dot.cpp
+++ b/lib/read_mealy_from_dot.cpp
@@ -14,8 +14,8 @@ T get(istream& in){
 	return t;
 }
 
-Mealy read_mealy_from_dot(istream& in){
-	Mealy m;
+mealy read_mealy_from_dot(istream& in){
+	mealy m;
 
 	string line;
 	stringstream ss;
@@ -57,7 +57,7 @@ Mealy read_mealy_from_dot(istream& in){
 	return m;
 }
 
-Mealy read_mealy_from_dot(const string& filename){
+mealy read_mealy_from_dot(const string& filename){
 	ifstream file(filename);
 	return read_mealy_from_dot(file);
 }
diff --git a/lib/read_mealy_from_dot.hpp b/lib/read_mealy_from_dot.hpp
index 1b8b55a..e73e8ba 100644
--- a/lib/read_mealy_from_dot.hpp
+++ b/lib/read_mealy_from_dot.hpp
@@ -2,6 +2,6 @@
 
 #include <iosfwd>
 
-struct Mealy;
-Mealy read_mealy_from_dot(const std::string & filename);
-Mealy read_mealy_from_dot(std::istream & input);
+struct mealy;
+mealy read_mealy_from_dot(const std::string & filename);
+mealy read_mealy_from_dot(std::istream & input);
diff --git a/lib/seperating_family.cpp b/lib/seperating_family.cpp
new file mode 100644
index 0000000..fbad30e
--- /dev/null
+++ b/lib/seperating_family.cpp
@@ -0,0 +1,48 @@
+#include "seperating_family.hpp"
+
+#include <functional>
+#include <stack>
+#include <utility>
+
+using namespace std;
+
+seperating_family create_seperating_family(const adaptive_distinguishing_sequence & sequence, const seperating_matrix & all_pair_seperating_sequences){
+	seperating_family seperating_family(all_pair_seperating_sequences.size());
+
+	stack<pair<word, reference_wrapper<const adaptive_distinguishing_sequence>>> work;
+	work.push({{}, sequence});
+
+	while(!work.empty()){
+		auto word = work.top().first;
+		const adaptive_distinguishing_sequence & node = work.top().second;
+		work.pop();
+
+		if(node.children.empty()){
+			// add sequence to this leave
+			for(auto && p : node.CI){
+				const auto state = p.second;
+				seperating_family[state.base()].push_back(word);
+			}
+
+			// if the leaf is not a singleton, we need the all_pair seperating seqs
+			for(auto && p : node.CI){
+				for(auto && q : node.CI){
+					const auto s = p.second;
+					const auto t = q.second;
+					if(s == t) continue;
+					seperating_family[s.base()].push_back(all_pair_seperating_sequences[s.base()][t.base()]);
+				}
+			}
+
+			continue;
+		}
+
+		for(auto && i : node.word)
+			word.push_back(i);
+
+		for(auto && c : node.children)
+			work.push({word, c});
+	}
+
+	return seperating_family;
+}
diff --git a/lib/seperating_family.hpp b/lib/seperating_family.hpp
new file mode 100644
index 0000000..ed54049
--- /dev/null
+++ b/lib/seperating_family.hpp
@@ -0,0 +1,17 @@
+#pragma once
+
+#include "adaptive_distinguishing_sequence.hpp"
+#include "seperating_matrix.hpp"
+#include "types.hpp"
+
+/*
+ * Given an (incomplete) adaptive distinguishing sequence and all pair
+ * seperating sequences, we can construct a seperating family (as defined
+ * in Lee & Yannakakis). If the adaptive distinguishing sequence is complete,
+ * then the all pair seperating sequences are not needed.
+ */
+
+using seperating_set = std::vector<word>;
+using seperating_family = std::vector<seperating_set>;
+
+seperating_family create_seperating_family(adaptive_distinguishing_sequence const & sequence, seperating_matrix const & all_pair_seperating_sequences);
diff --git a/lib/seperating_matrix.cpp b/lib/seperating_matrix.cpp
new file mode 100644
index 0000000..8a21e2a
--- /dev/null
+++ b/lib/seperating_matrix.cpp
@@ -0,0 +1,53 @@
+#include "seperating_matrix.hpp"
+
+#include <cassert>
+#include <functional>
+#include <queue>
+
+using namespace std;
+
+seperating_matrix create_all_pair_seperating_sequences(const splitting_tree & root){
+	const auto N = root.states.size();
+	seperating_matrix all_pair_seperating_sequences(N, seperating_row(N));
+
+	queue<reference_wrapper<const splitting_tree>> work;
+	work.push(root);
+
+	// total complexity is O(n^2), as we're visiting each pair only once :)
+	while(!work.empty()){
+		const splitting_tree & node = work.front();
+		work.pop();
+
+		auto it = begin(node.children);
+		auto ed = end(node.children);
+
+		while(it != ed){
+			auto jt = next(it);
+			while(jt != ed){
+				for(auto && s : it->states){
+					for(auto && t : jt->states){
+						assert(all_pair_seperating_sequences[t.base()][s.base()].empty());
+						assert(all_pair_seperating_sequences[s.base()][t.base()].empty());
+						all_pair_seperating_sequences[t.base()][s.base()] = node.seperator;
+						all_pair_seperating_sequences[s.base()][t.base()] = node.seperator;
+					}
+				}
+				jt++;
+			}
+			it++;
+		}
+
+		for(auto && c : node.children){
+			work.push(c);
+		}
+	}
+
+	for(size_t i = 0; i < N; ++i){
+		for(size_t j = 0; j < N; ++j){
+			if(i == j) continue;
+			assert(!all_pair_seperating_sequences[i][j].empty());
+		}
+	}
+
+	return all_pair_seperating_sequences;
+}
diff --git a/lib/seperating_matrix.hpp b/lib/seperating_matrix.hpp
new file mode 100644
index 0000000..b6d0d3c
--- /dev/null
+++ b/lib/seperating_matrix.hpp
@@ -0,0 +1,15 @@
+#pragma once
+
+#include "types.hpp"
+#include "splitting_tree.hpp"
+
+/*
+ * A seperating matrix is a matrix indexed by states, which assigns to each
+ * pair of (inequivalent) states a seperating sequences. This can be done by
+ * the classical Hopcroft algorithm
+ */
+
+using seperating_row = std::vector<word>;
+using seperating_matrix = std::vector<seperating_row>;
+
+seperating_matrix create_all_pair_seperating_sequences(splitting_tree const & root);
diff --git a/lib/create_splitting_tree.cpp b/lib/splitting_tree.cpp
similarity index 87%
rename from lib/create_splitting_tree.cpp
rename to lib/splitting_tree.cpp
index 95526b4..2b7ebb1 100644
--- a/lib/create_splitting_tree.cpp
+++ b/lib/splitting_tree.cpp
@@ -1,6 +1,7 @@
-#include "create_splitting_tree.hpp"
+#include "splitting_tree.hpp"
 #include "partition.hpp"
 
+#include <cassert>
 #include <functional>
 #include <numeric>
 #include <queue>
@@ -8,6 +9,21 @@
 
 using namespace std;
 
+splitting_tree::splitting_tree(size_t N, size_t depth)
+: states(N)
+, depth(depth)
+{
+	iota(begin(states), end(states), 0);
+}
+
+splitting_tree &lca_impl2(splitting_tree & node){
+	if(node.mark > 1) return node;
+	for(auto && c : node.children){
+		if(c.mark > 0) return lca_impl2(c);
+	}
+	return node; // this is a leaf
+}
+
 template <typename T>
 std::vector<T> concat(std::vector<T> const & l, std::vector<T> const & r){
 	std::vector<T> ret(l.size() + r.size());
@@ -16,7 +32,7 @@ std::vector<T> concat(std::vector<T> const & l, std::vector<T> const & r){
 	return ret;
 }
 
-result create_splitting_tree(const Mealy& g, options opt){
+result create_splitting_tree(const mealy& g, options opt){
 	const auto N = g.graph.size();
 	const auto P = g.input_indices.size();
 	const auto Q = g.output_indices.size();
@@ -30,12 +46,12 @@ result create_splitting_tree(const Mealy& g, options opt){
 	 * tree. We keep track of how many times we did no work. If this is too
 	 * much, there is no complete splitting tree.
 	 */
-	queue<reference_wrapper<splijtboom>> work;
+	queue<reference_wrapper<splitting_tree>> work;
 	size_t days_without_progress = 0;
 
 	// Some lambda functions capturing some state, makes the code a bit easier :)
 	const auto add_push_new_block = [&work](auto new_blocks, auto & boom) {
-		boom.children.assign(new_blocks.size(), splijtboom(0, boom.depth + 1));
+		boom.children.assign(new_blocks.size(), splitting_tree(0, boom.depth + 1));
 
 		auto i = 0;
 		for(auto && b : new_blocks){
@@ -69,7 +85,7 @@ result create_splitting_tree(const Mealy& g, options opt){
 	// We'll start with the root, obviously
 	work.push(root);
 	while(!work.empty()){
-		splijtboom & boom = work.front();
+		splitting_tree & boom = work.front();
 		work.pop();
 		const auto depth = boom.depth;
 
diff --git a/lib/splitting_tree.hpp b/lib/splitting_tree.hpp
index dfcf0ab..9dc6aef 100644
--- a/lib/splitting_tree.hpp
+++ b/lib/splitting_tree.hpp
@@ -2,27 +2,24 @@
 
 #include "mealy.hpp"
 
-#include <numeric>
-#include <type_traits>
-#include <vector>
+/*
+ * A splitting tree as defined in Lee & Yannakakis. The structure is also
+ * called a derivation tree in Knuutila. Both the classical Hopcroft algorithm
+ * and the Lee & Yannakakis algorithm produce splitting trees.
+ */
 
-struct splijtboom {
-	splijtboom(size_t N, size_t depth)
-	: states(N)
-	, depth(depth)
-	{
-		std::iota(begin(states), end(states), 0);
-	}
+struct splitting_tree {
+	splitting_tree(size_t N, size_t depth);
 
 	std::vector<state> states;
-	std::vector<splijtboom> children;
+	std::vector<splitting_tree> children;
 	std::vector<input> seperator;
 	size_t depth = 0;
 	mutable int mark = 0; // used for some algorithms...
 };
 
 template <typename Fun>
-void lca_impl1(splijtboom const & node, Fun && f){
+void lca_impl1(splitting_tree const & node, Fun && f){
 	node.mark = 0;
 	if(!node.children.empty()){
 		for(auto && c : node.children){
@@ -36,24 +33,57 @@ void lca_impl1(splijtboom const & node, Fun && f){
 	}
 }
 
-inline splijtboom & lca_impl2(splijtboom & node){
-	if(node.mark > 1) return node;
-	for(auto && c : node.children){
-		if(c.mark > 0) return lca_impl2(c);
-	}
-	return node; // this is a leaf
-}
+splitting_tree & lca_impl2(splitting_tree & node);
 
 template <typename Fun>
-splijtboom & lca(splijtboom & root, Fun && f){
+splitting_tree & lca(splitting_tree & root, Fun && f){
 	static_assert(std::is_same<decltype(f(0)), bool>::value, "f should return a bool");
 	lca_impl1(root, f);
 	return lca_impl2(root);
 }
 
 template <typename Fun>
-const splijtboom & lca(const splijtboom & root, Fun && f){
+const splitting_tree & lca(const splitting_tree & root, Fun && f){
 	static_assert(std::is_same<decltype(f(0)), bool>::value, "f should return a bool");
 	lca_impl1(root, f);
-	return lca_impl2(const_cast<splijtboom&>(root));
+	return lca_impl2(const_cast<splitting_tree&>(root));
 }
+
+
+/*
+ * The algorithm to create a splitting tree can be altered in some ways. This
+ * struct provides options to the algorithm. There are two common setups.
+ */
+
+struct options {
+	bool check_validity = true;
+	bool cache_succesors = true;
+};
+
+constexpr options lee_yannakakis_style{true, true};
+constexpr options hopcroft_style{false, false};
+
+
+/*
+ * The algorithm to create a splitting tree also produces some other useful
+ * data. This struct captures exactly that.
+ */
+
+struct result {
+	result(size_t N)
+	: root(N, 0)
+	, successor_cache()
+	, is_complete(true)
+	{}
+
+	// The splitting tree as described in Lee & Yannakakis
+	splitting_tree root;
+
+	// Encodes f_u : depth -> state -> state, where only the depth of u is of importance
+	std::vector<std::vector<state>> successor_cache;
+
+	// false <-> no adaptive distinguishing sequence
+	bool is_complete;
+};
+
+result create_splitting_tree(mealy const & m, options opt);
diff --git a/lib/transfer_sequences.cpp b/lib/transfer_sequences.cpp
new file mode 100644
index 0000000..9a3d36c
--- /dev/null
+++ b/lib/transfer_sequences.cpp
@@ -0,0 +1,42 @@
+#include "transfer_sequences.hpp"
+
+#include "mealy.hpp"
+
+#include <queue>
+
+using namespace std;
+
+transfer_sequences create_transfer_sequences(const mealy& machine, state s){
+	vector<bool> visited(machine.graph_size, false);
+	vector<word> words(machine.graph_size);
+
+	queue<state> work;
+	work.push(s);
+	while(!work.empty()){
+		const auto u = work.front();
+		work.pop();
+
+		if(visited[u.base()]) continue;
+
+		visited[u.base()] = true;
+
+		for(input i = 0; i < machine.input_size; ++i){
+			const auto v = apply(machine, u, i).to;
+			if(visited[v.base()]) continue;
+
+			words[v.base()] = words[u.base()];
+			words[v.base()].push_back(i);
+			work.push(v);
+		}
+	}
+
+	return words;
+}
+
+std::vector<transfer_sequences> create_all_transfer_sequences(const mealy& machine){
+	vector<transfer_sequences> transfer_sequences(machine.graph_size);
+	for(state s = 0; s < machine.graph_size; ++s){
+		transfer_sequences[s.base()] = create_transfer_sequences(machine, s);
+	}
+	return transfer_sequences;
+}
diff --git a/lib/transfer_sequences.hpp b/lib/transfer_sequences.hpp
new file mode 100644
index 0000000..95e2d36
--- /dev/null
+++ b/lib/transfer_sequences.hpp
@@ -0,0 +1,10 @@
+#pragma once
+
+#include "types.hpp"
+
+struct mealy;
+
+using transfer_sequences = std::vector<word>;
+
+transfer_sequences create_transfer_sequences(mealy const & machine, state s);
+std::vector<transfer_sequences> create_all_transfer_sequences(mealy const & machine);
diff --git a/lib/types.hpp b/lib/types.hpp
new file mode 100644
index 0000000..a097dcf
--- /dev/null
+++ b/lib/types.hpp
@@ -0,0 +1,14 @@
+#pragma once
+
+#include "phantom.hpp"
+
+#include <vector>
+
+/* We use size_t's for easy indexing. But we do not want to mix states and
+ * inputs. We use phantom typing to "generate" distinguished types :).
+ */
+using state = phantom<size_t, struct state_tag>;
+using input = phantom<size_t, struct input_tag>;
+using output = phantom<size_t, struct output_tag>;
+
+using word = std::vector<input>;
diff --git a/lib/write_tree_to_dot.cpp b/lib/write_tree_to_dot.cpp
index fe586ae..ce3cc18 100644
--- a/lib/write_tree_to_dot.cpp
+++ b/lib/write_tree_to_dot.cpp
@@ -1,5 +1,5 @@
 #include "write_tree_to_dot.hpp"
-#include "create_adaptive_distinguishing_sequence.hpp"
+#include "adaptive_distinguishing_sequence.hpp"
 #include "splitting_tree.hpp"
 
 #include <fstream>
@@ -17,8 +17,8 @@ ostream & operator<<(ostream& out, vector<T> const & x){
 }
 
 
-void write_splitting_tree_to_dot(const splijtboom& root, ostream& out){
-	write_tree_to_dot(root, [](const splijtboom & node, ostream& out){
+void write_splitting_tree_to_dot(const splitting_tree& root, ostream& out){
+	write_tree_to_dot(root, [](const splitting_tree & node, ostream& out){
 		out << node.states;
 		if(!node.seperator.empty()){
 			out << "\\n" << node.seperator;
@@ -26,13 +26,13 @@ void write_splitting_tree_to_dot(const splijtboom& root, ostream& out){
 	}, out);
 }
 
-void write_splitting_tree_to_dot(const splijtboom& root, const string& filename){
+void write_splitting_tree_to_dot(const splitting_tree& root, const string& filename){
 	ofstream file(filename);
 	write_splitting_tree_to_dot(root, file);
 }
 
-void write_adaptive_distinguishing_sequence_to_dot(const distinguishing_sequence & root, ostream & out){
-	write_tree_to_dot(root, [](const distinguishing_sequence & node, ostream& out){
+void write_adaptive_distinguishing_sequence_to_dot(const adaptive_distinguishing_sequence & root, ostream & out){
+	write_tree_to_dot(root, [](const adaptive_distinguishing_sequence & node, ostream& out){
 		if(!node.word.empty()){
 			out << node.word;
 		} else {
@@ -43,7 +43,7 @@ void write_adaptive_distinguishing_sequence_to_dot(const distinguishing_sequence
 	}, out);
 }
 
-void write_adaptive_distinguishing_sequence_to_dot(const distinguishing_sequence & root, string const & filename){
+void write_adaptive_distinguishing_sequence_to_dot(const adaptive_distinguishing_sequence & root, string const & filename){
 	ofstream file(filename);
 	write_adaptive_distinguishing_sequence_to_dot(root, file);
 }
diff --git a/lib/write_tree_to_dot.hpp b/lib/write_tree_to_dot.hpp
index 2c957fc..a0906fa 100644
--- a/lib/write_tree_to_dot.hpp
+++ b/lib/write_tree_to_dot.hpp
@@ -36,10 +36,10 @@ void write_tree_to_dot(const T & tree, NodeString && node_string, std::ostream &
 
 
 // Specialized printing for splitting trees and dist seqs
-struct splijtboom;
-void write_splitting_tree_to_dot(const splijtboom & root, std::ostream & out);
-void write_splitting_tree_to_dot(const splijtboom & root, std::string const & filename);
+struct splitting_tree;
+void write_splitting_tree_to_dot(const splitting_tree & root, std::ostream & out);
+void write_splitting_tree_to_dot(const splitting_tree & root, std::string const & filename);
 
-struct distinguishing_sequence;
-void write_adaptive_distinguishing_sequence_to_dot(const distinguishing_sequence & root, std::ostream & out);
-void write_adaptive_distinguishing_sequence_to_dot(const distinguishing_sequence & root, std::string const & filename);
+struct adaptive_distinguishing_sequence;
+void write_adaptive_distinguishing_sequence_to_dot(const adaptive_distinguishing_sequence & root, std::ostream & out);
+void write_adaptive_distinguishing_sequence_to_dot(const adaptive_distinguishing_sequence & root, std::string const & filename);
diff --git a/src/conf.cpp b/src/conf.cpp
index 99e1c0a..78f3388 100644
--- a/src/conf.cpp
+++ b/src/conf.cpp
@@ -1,9 +1,7 @@
 #include <mealy.hpp>
 #include <read_mealy_from_dot.hpp>
 
-#include <boost/iostreams/device/file_descriptor.hpp>
-#include <boost/iostreams/filtering_stream.hpp>
-#include <boost/iostreams/filter/gzip.hpp>
+#include <io.hpp>
 
 #include <fstream>
 #include <iostream>
@@ -11,40 +9,68 @@
 
 using namespace std;
 
-int main(int argc, char *argv[]){
-	if(argc != 3) return 37;
-
-	const string m_filename = argv[1];
-	const string c_filename = argv[2];
-
-	ifstream m_file(m_filename);
-	boost::iostreams::filtering_istream c_file;
-	c_file.push(boost::iostreams::gzip_decompressor());
-	c_file.push(boost::iostreams::file_descriptor_source(c_filename));
-
-	const auto machine = read_mealy_from_dot(m_file);
-
-	string in;
-	string out;
-
-	state s = 0;
-	size_t count = 0;
-	while(c_file >> in >> out){
-		const auto i = machine.input_indices.at(in);
-		const auto o = machine.output_indices.at(out);
-
-		const auto ret = apply(machine, s, i);
-		if(ret.output != o){
-			cout << "conformance fail" << endl;
-			cout << ret.output << " != " << o << endl;
-			cout << "at index " << count << endl;
-			return 1;
-		}
-
-		s = ret.to;
-		count++;
+template <typename T>
+vector<string> create_reverse_map(map<string, T> const & indices){
+	vector<string> ret(indices.size());
+	for(auto&& p : indices){
+		ret[p.second.base()] = p.first;
 	}
-
-	cout << "conformance succes " << count << endl;
+	return ret;
+}
+
+int main(int argc, char *argv[]){
+	if(argc != 4) return 37;
+
+	const string spec_filename = argv[1];
+	const string impl_filename = argv[2];
+	const string suite_filename = argv[3];
+
+	ifstream spec_file(spec_filename);
+	ifstream impl_file(impl_filename);
+
+	boost::iostreams::filtering_istream suite_file;
+	suite_file.push(boost::iostreams::gzip_decompressor());
+	suite_file.push(boost::iostreams::file_descriptor_source(suite_filename));
+	boost::archive::text_iarchive archive(suite_file);
+
+	const auto spec = read_mealy_from_dot(spec_file);
+	const auto impl = read_mealy_from_dot(impl_file);
+
+	const auto spec_o_map = create_reverse_map(spec.output_indices);
+	const auto impl_o_map = create_reverse_map(impl.output_indices);
+
+	vector<vector<string>> suite;
+	archive >> suite;
+
+	size_t tcount = 0;
+	for(auto && test : suite){
+		state s = 0;
+		state t = 0;
+
+		size_t count = 0;
+		for(auto && i : test){
+			const auto i1 = spec.input_indices.at(i);
+			const auto r1 = apply(spec, s, i1);
+			const auto o1 = spec_o_map[r1.output.base()];
+			s = r1.to;
+
+			const auto i2 = spec.input_indices.at(i);
+			const auto r2 = apply(impl, t, i2);
+			const auto o2 = spec_o_map[r2.output.base()];
+			t = r2.to;
+
+			if(o1 != o2){
+				cout << "conformance fail" << endl;
+				cout << o1 << " != " << o2 << endl;
+				cout << "at test " << tcount << endl;
+				cout << "at char " << count << endl;
+				return 1;
+			}
+			count++;
+		}
+		tcount++;
+	}
+
+	cout << "conformance succes " << tcount << endl;
 }
 
diff --git a/src/main.cpp b/src/main.cpp
index dc29e4b..22daa3b 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -1,20 +1,15 @@
-#include <create_adaptive_distinguishing_sequence.hpp>
-#include <create_splitting_tree.hpp>
+#include <adaptive_distinguishing_sequence.hpp>
 #include <logging.hpp>
+#include <mealy.hpp>
 #include <read_mealy_from_dot.hpp>
-#include <write_tree_to_dot.hpp>
+#include <seperating_family.hpp>
+#include <seperating_matrix.hpp>
+#include <splitting_tree.hpp>
+#include <transfer_sequences.hpp>
 
-#include <boost/iostreams/device/file_descriptor.hpp>
-#include <boost/iostreams/filter/gzip.hpp>
-#include <boost/iostreams/filtering_stream.hpp>
+#include <io.hpp>
 
-#include <cassert>
-#include <fstream>
-#include <functional>
-#include <iostream>
-#include <stack>
-#include <utility>
-#include <vector>
+#include <future>
 
 using namespace std;
 
@@ -27,31 +22,26 @@ vector<string> create_reverse_map(map<string, T> const & indices){
 	return ret;
 }
 
-auto bfs(Mealy const & machine, state s){
-	vector<bool> visited(machine.graph_size, false);
-	vector<vector<input>> words(machine.graph_size);
+template <typename T>
+std::vector<T> concat(std::vector<T> const & l, std::vector<T> const & r){
+	std::vector<T> ret(l.size() + r.size());
+	auto it = copy(begin(l), end(l), begin(ret));
+	copy(begin(r), end(r), it);
+	return ret;
+}
 
-	queue<state> work;
-	work.push(s);
-	while(!work.empty()){
-		const auto u = work.front();
-		work.pop();
-
-		if(visited[u.base()]) continue;
-
-		visited[u.base()] = true;
-
-		for(input i = 0; i < machine.input_size; ++i){
-			const auto v = apply(machine, u, i).to;
-			if(visited[v.base()]) continue;
-
-			words[v.base()] = words[u.base()];
-			words[v.base()].push_back(i);
-			work.push(v);
+template <typename T>
+std::vector<std::vector<T>> all_seqs(T min, T max, std::vector<std::vector<T>> const & seqs){
+	std::vector<std::vector<T>> ret((max - min) * seqs.size());
+	auto it = begin(ret);
+	for(auto && x : seqs){
+		for(T i = min; i < max; ++i){
+			it->assign(x.size()+1);
+			auto e = copy(x.begin(), x.end(), it->begin());
+			*e++ = i;
 		}
 	}
-
-	return words;
+	return ret;
 }
 
 int main(int argc, char *argv[]){
@@ -63,218 +53,85 @@ int main(int argc, char *argv[]){
 		return read_mealy_from_dot(filename);
 	}();
 
-	const auto splitting_tree_hopcroft = [&]{
-		timer t("creating hopcroft splitting tree");
-		return create_splitting_tree(machine, without_validity_check);
-	}();
+	auto all_pair_seperating_sequences_fut = async([&]{
+		const auto splitting_tree_hopcroft = [&]{
+			timer t("creating hopcroft splitting tree");
+			return create_splitting_tree(machine, hopcroft_style);
+		}();
 
-	const auto all_pair_seperating_sequences = [&]{
-		timer t("gathering all seperating sequences");
-
-		vector<vector<vector<input>>> all_pair_seperating_sequences(machine.graph_size, vector<vector<input>>(machine.graph_size));
-
-		queue<reference_wrapper<const splijtboom>> work;
-		work.push(splitting_tree_hopcroft.root);
-
-		// total complexity is O(n^2), as we're visiting each pair only once :)
-		while(!work.empty()){
-			const splijtboom & node = work.front();
-			work.pop();
-
-			auto it = begin(node.children);
-			auto ed = end(node.children);
-
-			while(it != ed){
-				auto jt = next(it);
-				while(jt != ed){
-					for(auto && s : it->states){
-						for(auto && t : jt->states){
-							assert(all_pair_seperating_sequences[t.base()][s.base()].empty());
-							assert(all_pair_seperating_sequences[s.base()][t.base()].empty());
-							all_pair_seperating_sequences[t.base()][s.base()] = node.seperator;
-							all_pair_seperating_sequences[s.base()][t.base()] = node.seperator;
-						}
-					}
-					jt++;
-				}
-				it++;
-			}
-
-			for(auto && c : node.children){
-				work.push(c);
-			}
-		}
-
-		for(size_t i = 0; i < machine.graph_size; ++i){
-			for(size_t j = 0; j < machine.graph_size; ++j){
-				if(i == j) continue;
-				assert(!all_pair_seperating_sequences[i][j].empty());
-			}
-		}
+		const auto all_pair_seperating_sequences = [&]{
+			timer t("gathering all seperating sequences");
+			return create_all_pair_seperating_sequences(splitting_tree_hopcroft.root);
+		}();
 
 		return all_pair_seperating_sequences;
-	}();
+	});
 
-	const auto splitting_tree = [&]{
-		timer t("Lee & Yannakakis I");
-		return create_splitting_tree(machine, with_validity_check);
-	}();
+	auto sequence_fut = async([&]{
+		const auto splitting_tree = [&]{
+			timer t("Lee & Yannakakis I");
+			return create_splitting_tree(machine, lee_yannakakis_style);
+		}();
 
-	if(false){
-		timer t("writing splitting tree");
-		const string tree_filename = splitting_tree.is_complete ? (filename + ".splitting_tree") : (filename + ".incomplete_splitting_tree");
-		write_splitting_tree_to_dot(splitting_tree.root, tree_filename);
-	}
+		const auto sequence = [&]{
+			timer t("Lee & Yannakakis II");
+			return create_adaptive_distinguishing_sequence(splitting_tree);
+		}();
 
-	const auto sequence = [&]{
-		timer t("Lee & Yannakakis II");
-		return create_adaptive_distinguishing_sequence(splitting_tree);
-	}();
+		return sequence;
+	});
 
-	if(false){
-		timer t("writing dist sequence");
-		const string dseq_filename = splitting_tree.is_complete ? (filename + ".dist_seq") : (filename + ".incomplete_dist_seq");
-		write_adaptive_distinguishing_sequence_to_dot(sequence, dseq_filename);
-	}
+	auto transfer_sequences_fut = std::async([&]{
+		timer t("determining transfer sequences");
+		return create_transfer_sequences(machine, 0);
+	});
+
+	const auto all_pair_seperating_sequences = all_pair_seperating_sequences_fut.get();
+	const auto sequence = sequence_fut.get();
 
 	const auto seperating_family = [&]{
 		timer t("making seperating family");
-		using Word = vector<input>;
-		using SepSet = vector<Word>;
-		vector<SepSet> seperating_family(machine.graph_size);
-
-		stack<pair<vector<input>, reference_wrapper<const distinguishing_sequence>>> work;
-		work.push({{}, sequence});
-
-		while(!work.empty()){
-			auto word = work.top().first;
-			const distinguishing_sequence & node = work.top().second;
-			work.pop();
-
-			if(node.children.empty()){
-				// add sequence to this leave
-				for(auto && p : node.CI){
-					const auto state = p.second;
-					seperating_family[state.base()].push_back(word);
-				}
-
-				// if the leaf is not a singleton, we need the all_pair seperating seqs
-				for(auto && p : node.CI){
-					for(auto && q : node.CI){
-						const auto s = p.second;
-						const auto t = q.second;
-						if(s == t) continue;
-						seperating_family[s.base()].push_back(all_pair_seperating_sequences[s.base()][t.base()]);
-					}
-				}
-
-				continue;
-			}
-
-			for(auto && i : node.word)
-				word.push_back(i);
-
-			for(auto && c : node.children)
-				work.push({word, c});
-		}
-
-		return seperating_family;
+		return create_seperating_family(sequence, all_pair_seperating_sequences);
 	}();
 
+	const auto transfer_sequences = transfer_sequences_fut.get();
 	const auto inputs = create_reverse_map(machine.input_indices);
 	const auto outputs = create_reverse_map(machine.output_indices);
-	const auto print_uio = [&](auto const & word, auto & out, state s) -> auto & {
-		for(auto && i : word){
-			const auto o = apply(machine, s, i);
-			s = o.to;
 
-			out << inputs[i.base()] << ' ' << outputs[o.output.base()] << '\n';
-		}
-		return out;
-	};
+	{
+		timer t("making test suite");
+		vector<word> suite;
 
-	const auto transfer_sequences = [&]{
-		timer t("determining transfer sequences");
-		vector<vector<vector<input>>> transfer_sequences(machine.graph_size);
 		for(state s = 0; s < machine.graph_size; ++s){
-			transfer_sequences[s.base()] = bfs(machine, s);
-		}
-		return transfer_sequences;
-	}();
+			const auto prefix = transfer_sequences[s.base()];
 
-	const auto short_checking_seq = [&]{
-		timer t("making short checking seq");
-		vector<input> big_seq;
-		state from = 0;
-		for(state s = from; s < machine.graph_size; ++s){
-			for(const auto & seq : seperating_family[s.base()]){
-				copy(begin(seq), end(seq), back_inserter(big_seq));
-				from = apply(machine, s, begin(seq), end(seq)).to;
-
-				const auto to = s;
-				if(from == to) continue;
-
-				const auto transfer = transfer_sequences[from.base()][to.base()];
-				copy(begin(transfer), end(transfer), back_inserter(big_seq));
-			}
-
-			const auto to = s+1;
-			if(from == to) continue;
-
-			const auto transfer = transfer_sequences[from.base()][to.base()];
-			copy(begin(transfer), end(transfer), back_inserter(big_seq));
-		}
-
-		return big_seq;
-	}();
-
-	{
-		timer t("writing short checking seq");
-		const string uios_filename = filename + ".short_check_seq";
-
-		boost::iostreams::filtering_ostream out;
-		out.push(boost::iostreams::gzip_compressor());
-		out.push(boost::iostreams::file_descriptor_sink(uios_filename));
-
-		print_uio(short_checking_seq, out, 0);
-	}
-
-	const auto long_checking_seq = [&]{
-		timer t("making long checking seq");
-		vector<input> big_seq;
-		state from = 0;
-		for(state s = from; s < machine.graph_size; ++s){
-			for(input i = 0; i < machine.input_size; ++i){
-				const auto t = apply(machine, s, i).to;
-
-				for(auto && seq : seperating_family[t.base()]){
-					if(from != s){
-						const auto transfer = transfer_sequences[from.base()][s.base()];
-						copy(begin(transfer), end(transfer), back_inserter(big_seq));
-						from = s;
-					}
-
-					big_seq.push_back(i);
-					from = t;
-
-					copy(begin(seq), end(seq), back_inserter(big_seq));
-					from = apply(machine, from, begin(seq), end(seq)).to;
-				}
+			for(auto && suffix : seperating_family[s.base()]){
+				suite.push_back(concat(prefix, suffix));
 			}
 		}
 
-		return big_seq;
-	}();
+		vector<vector<string>> real_suite(suite.size());
+		transform(suite.begin(), suite.end(), real_suite.begin(), [&inputs](auto const & seq){
+			vector<string> seq2(seq.size());
+			transform(seq.begin(), seq.end(), seq2.begin(), [&inputs](auto const & i){
+				return inputs[i.base()];
+			});
+			return seq2;
+		});
 
-	{
-		timer t("writing long checking seq");
-		const string uios_filename = filename + ".full_check_seq";
+//		for(auto && test : real_suite) {
+//			for(auto && s : test) {
+//				cout << s << " ";
+//			}
+//			cout << endl;
+//		}
 
-		boost::iostreams::filtering_ostream out;
-		out.push(boost::iostreams::gzip_compressor());
-		out.push(boost::iostreams::file_descriptor_sink(uios_filename));
+		boost::iostreams::filtering_ostream compressed_stream;
+		compressed_stream.push(boost::iostreams::gzip_compressor());
+		compressed_stream.push(boost::iostreams::file_descriptor_sink("test_suite"));
 
-		print_uio(long_checking_seq, out, 0);
+		boost::archive::text_oarchive archive(compressed_stream);
+		archive << real_suite;
 	}
 }
 
diff --git a/src/stats.cpp b/src/stats.cpp
index bb60817..5d651b7 100644
--- a/src/stats.cpp
+++ b/src/stats.cpp
@@ -1,7 +1,6 @@
 #include <read_mealy_from_dot.hpp>
 #include <mealy.hpp>
 
-#include <string>
 #include <fstream>
 #include <iostream>