Linear Time Construction of

Suffix Tree
Presented By
Dr. Shazzad Hosain
Asst. Prof. EECS, NSU
 High-level of Ukkonen’s Algorithm
• Ukkonen’s algorithm is divided into m phases. In phase i+1,
tree i+1 is constructed from i
• Each phase i+1 is further divided into i+1 extensions, one for
each of the i+1 suffixes of S[1… i+1].
ab b

phases
a
: S[1…1] {a}
1
b b
2 : S[1…2] {ab, b}
a
3 : S[1…3] {aba, ba, a} a

extensions 1 2
 1234567890 How suffix links help?
MISSISSIPI
P
M I
S
9
10: MISSISSIPI I
I
S S
9 : MISSISSIP S
S S P I I
8 : MISSISSI I P I
S I I 6
S
7 : MISSISS S 8 S
S S
6 : MISSIS P I P S
S P I I
5 : MISSI I I P
I 7
4 : MISS 1 I P I
P
3 : MIS I 5 I
2 : MI 3
2 4
1 : M
Corollary 6.1.1: In Ukkanon’s algorithm, any newly created internal
node will have a suffix link form it by the end of the next extension.
What is achieved so far?

Not so much. Worst-case running

time is O(m2) for a phase.
 Trick1: Skip/Count Trick

There must be a γ path from s(v).

 Trick1: Skip/Count Trick
Walking down along γ takes time
proportional to |γ|

Skip/count trick reduces the traversal

time to something proportional to the
number of nodes on the path.

zabcdefghy
Nodes
Edge length 2 2 3 3

But what does it buy in terms of

worst-case bounds?

There must be a γ path from s(v).

Lemma 6.1.2: Let (v, s(v)) be any suffix link traversed during
Ukkonen’s algorithm. At that moment , the node-depth of v is
at most one greater than the node depth of s(v).

v=2 s(v)=1

s(v)=3
v=3

v=4 s(v)=5
 Lemma 6.1.2: Let (v, s(v)) be any suffix link traversed during
Ukkonen’s algorithm. At that moment , the node-depth of v is
at most one greater than the node depth of s(v).

Theorem 6.1.1: Using the skip/count trick, any phase of

Ukkonen’s algorithm takes O(m) time.
In a single extension
– The algorithm walks up at most one edge
– Find suffix link and traverse it
– Walks down some number of nodes
– Applies suffix extension rules
– And may add a suffix link

All operations except down-walk takes constant time

Only needs to analyze down walk time
 Lemma 6.1.2: Let (v, s(v)) be any suffix link traversed during
Ukkonen’s algorithm. At that moment , the node-depth of v is
at most one greater than the node depth of s(v).

Theorem 6.1.1: Using the skip/count trick, any phase of

Ukkonen’s algorithm takes O(m) time.
In a single extension
– The algorithm walks up at most one edge
– Find suffix link and traverse it
– Walks down some number of nodes
– Applies suffix extension rules
– And may add a suffix link
All operations except down-walk takes constant time
Only needs to analyze down walk time
– Decreases current node-depth by at most one
– Decreases node-depth by at most another one
– Each down walk moves to greater node-depth
– Over the entire phase, current node-depth is
decremented by at most 2m times
– Since no node can have depth greater than m,
the total possible increment to current node-
depth is bounded by 3m over the entire phase
– Total number of edge traversal bounded by 3m
– Since each edge traversal is constant, in a phase
all the down-walking is O(m).
 Complexity
• There are m phases
• Each phase takes O(m)
• So the running time is O(m2)

Two more tricks and we are done

 Simple Implementation Detail
• Suffix tree may require O(m2) space
• Consider the string
• Every suffix begins with a distinct character, so there
are 26 edges out of the root.
• Requires 26x27/2 characters in all
• So O(m) is impossible to achieve in this
representation.
 Alternative Representation of Suffix Tree
Edge Label Compression

1 2 3 4 56789 0 1 2

Could be 8,9

A fragment of the suffix tree Edge label compressed

Number of edge at most 2m – 1, and two numbers are written in an edge, so space is O(m)
 7 : 1234567
1234567890
MISSISSIPI 8 : 12345678
M S
I
I
S S S
S S I I
8 : MISSISSI I
I
S S
7 : MISSISS S S
S S
6 : MISSIS I
S
S
I
5 : MISSI I
Explicit Extension I

4 : MISS 1
3 : MIS
2 : MI 2
Implicit extension 3
4
1 : M

Observation 1: Rule 2 is a show stopper. We stop further extension.

 7 : 1234567
1234567890
MISSISSIPI 8 : 12345678
M S
I
I
S S S
S S I I
8 : MISSISSI I
I
1,7 S S
7 : MISSISS S S
S S 3,7
6 : MISSIS 2,7
S
4,7 S

5 : MISSI Explicit Extension

The major cost
4 : MISS 1
3 : MIS
2 : MI 2 e=8 3
4
1 : M
Observation 2: Once a leaf always a leaf
 7 : 1234567
1234567890
MISSISSIPI 8 : 12345678
M S
I
I
S S S
S S I I
8 : MISSISSI I
I
1,7 S S
7 : MISSISS S S
S S 3,7
6 : MISSIS 2,7
S
4,7 S

5 : MISSI Explicit Extension

The major cost
4 : MISS 1
3 : MIS
2 : MI 2 e=8 3
4
1 : M
Once a leaf always a leaf

At any phase the cost is only for explicit extension

 : 12345678
1234567890 8

MISSISSIPI 9 : 123456789
P 9,9
M S
I 9
I
9 : MISSISSIP S S S
S P I 9,9
2,5 S I
8 : MISSISSI I
I
9,9 P
S 6
7 : MISSISS 1,9 S 8 S
S
I S S 3,9
6 : MISSIS 2,9
6,9
S
P P S 4,9
I
9,9 9,9
5 : MISSI I
I
7
4 : MISS 1 5

3 : MIS
2 : MI 2 e=9 3
4
1 : M
Once a leaf always a leaf

At any phase the cost is only for explicit extension

 : 12345
1234567890 8

MISSISSIPI 9 : 123456789

Since there are only m phases, the total number of explicit

extension is bounded by 2m

So the total number of down-walk is bounded by O(m)

Or
The time to construct the suffix tree is bounded by O(m)
 Reference
• Chapter 6: Algorithms on Strings, Trees and
Sequences