Sorting Unsigned Permutations by Reversals using
Multi-Objective Evolutionary Algorithms with
Variable Size Individuals
Ahmadreza Ghaffarizadeh, Kamilia Ahmadi and Nicholas S. Flann
Computer Science Department, Utah State University, Logan Utah 84322-4205
Email: {ghaffarizadeh, k.ahmadi}@aggiemail.usu.edu, nick.flann@usu.edu
Abstract—Sorting by reversals is a simplified version of the
genome rearrangement problem that seeks to discover the evo-
lutionary relationship between different genomes, and is one of
the many challenging problems in Bioinformatics. Solving the
problem optimally has been proved to be NP-Hard and so a
selection of approximation algorithms have been developed. In
this paper a new mapping order is introduced to solve the
problem of sorting unsigned permutations using a specialized
multi-objective genetic algorithm. Our modified genetic algorithm
uses a population with variable length individuals to maintain a
worst time running time complexity of O(n4 log2 n), where n
is the problem size. The results show that this approach is more
effective than the 3/2 heuristic method and previous genetic
algorithm approaches.
Index Terms—Sorting by reversals, genome rearrangement,
sorting unsigned permutations, variable size individuals, multi-
objective genetic algorithm
I. I NTRODUCTION
Analysis of genome rearrangements in molecular evolution
was pioneered by Dobzhansky and Sturtevant in 1938, who
published a milestone paper with an evolutionary tree pre-
senting a rearrangement scenario with 17 inversions linking
the species D. pseudoobscura and D. Miranda [1] [2]. Every
genome rearrangement study involves solving a combinato-
rial puzzle to find a series of genome rearrangements that
transform one genome into another [3]. Reversal is the most
commonly observed mechanism in rearrangement of genes
and this makes sorting by reversal to be one of the most
challenging problems in bioinformatics in past decade.
In their simplest form, rearrangement events can be modeled
by series of reversals that transform one genome to another
[3]. The order of genes in a genome can be represented by a
permutation Π = hπ1 , π2 , π3 . . . πn i, where n is the number
of genes and πi is the gene id in position i. This problem is
reduced to sorting by reversals problem that can be described
as: given a permutation Π, find a shortest series of reversals
hρ1 ρ2 . . . ρm i that transforms it into the identity permutation.
To solve this problem, we introduce the breakpoint distance of
a permutation to assess the progress of the algorithm towards
the solution. We call a pair of neighboring elements πi and
πi+1 ∈ Π, with 0 ≤ i ≤ n an adjacency if πi and πi+1 , are
consecutive numbers, otherwise we call the pair a breakpoint.
Then the breakpoint distance is the number of breakpoints
in a permutation. Note that we add to π0 = 0 the start and
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πn+1 = n + 1 to the end of each permutation to count the
breakpoints at the start and end of permutation accordingly.
As the goal identity permutation has no breakpoints, sorting
by reversals corresponds to finding a series of reversals that
eliminates all breakpoints.
There are two types of permutations, signed and unsigned.
For signed permutations each πi has a positive or negative sign
reflecting the orientation of that block of genes in genome.
The problem of sorting a signed permutation by reversals can
be solved sub-optimally in O(n2 ) time [4], with the number
of reversal steps no greater than 3× the optimal solution [2].
However, having signed permutations is not always possible
due to limitations in equipment and costs, so at this time the
application of sorting by reversals to the unsigned permutation
problem has wider applicability.
From a combinatorial mathematics point-of-view, identify-
ing the optimal sequence of reversals for sorting of unsigned
permutations is an NP-Hard problem [5], therefore error
bounded heuristic solutions have been proposed [2] [6] [7].
The lowest guaranteed error bound thus far is the 1.375
algorithm proposed by Berman et al [8], meaning that the
length of the sequence found will be within 1.375× the length
of the optimal sequence. Auyeung and Abraham [9] suggested
a genetic algorithm (GA) approach to solve the problem by
mapping the unsigned reversal problem into 2n possible signed
reversal problems, then using the GA to heuristically search
this combinatorial space. Results showed that their method
was effective in many cases, but the estimated time complexity
of their method was O(n5 ). Here we use a modified version
of the standard GA that employs different size individuals
to decrease the running time of algorithm such that it takes
O(n4 log2 n) in the worst case, but empirical studies demon-
strate that the performance is considerably reduced in the
average case. It is difficult to determine a guaranteed bound for
our algorithm since it is stochastic, however as our empirical
results show, the method works well for smaller permutation
problems.
The rest of this paper is organized as follow: in Section 2
our proposed method is explained and our modified genetic
algorithm is described in detail by defining specific crossover
and mutation operators. Results are presented in Section 3 and
finally we conclude the paper with some discussion about our
proposed method and a future open research problems.
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 The genetic algorithm attempts to solve this problem by bal-
ancing these two competing objectives in its fitness function.
Given two individual solutions χxi and χyj , i is selected over j
probabilistically when i dominates j, or in other words, when
x < y (i is shorter than j) and B(Πi ) < B(Πj ). The method
(a) follows the framework of the standard genetic algorithm, but
uses special mutation and crossover operators that extend
and shrink the number and arrangement of reversals in each
solution:
• Create an initial random population with size n log n and
containing a diversity of short individuals and set it as the
current population. The maximum length of each reversal
(b)
sequence is set to 10% of the input permutation length,
n.
• Evaluate current population with the two objective func-
tions; the result will be the breakpoint distance of each
individual and its length.
• Select the best individuals (individuals with smallest
(c) breakpoint distance and length based on domination)
from current population. These individuals can be of
Fig. 1. Different crossover operators used in the method. (a) Regular 2-points different sizes.
crossover; (b) Absorption crossover; (c) Adjunction crossover
• Apply the modified crossover (see below) on this selected
individuals to create new offspring.
II. M ETHOD • Apply the modified mutation (see below) on these off-

The method utilizes a genetic algorithm approach that spring.

• Select between new generated offspring and parents in
searches the space of all possible sequences of reversals.
Search is guided by two complementary objectives: mini- population to create new population and set it as current
mizing the length of reversals in the current solution and population.
minimizing the estimated number of reversals needed to The algorithm terminates with success when an individual
complete the solution. Since each solution is a particular is found where B = 0; the algorithm terminates with failure
sequence of reversals, the first objective is simply the length if the maximum number of allowable steps is exceeded. In
of the solution. The second objective is more computationally this case the algorithm can be re-run with a new random
intensive because all the reversals in the solution have to be population.
applied before the number of breakpoints in the resulting A. Genetic Search Operators
permutation can be calculated. Before more details of the
This work utilizes a distinct set of genetic operators that are
search method are given, first we define a reversal and a
tailored to this problem. Specifically, the length of the reverse
solution.
sequences must be allowed to grow so a solution can have
Given an example permutation Πt at step t of the algorithm:
the potential to reduce the breakpoints to zero; conversely, the
π1 π2 π3 π4 π5 π6 solution must be allowed to shrink to optimize the length of
5 1 3 6 4 2 the reversal sequence. Below briefly describes the crossover
then if a single reversal ρ5,2 is applied, the permutation operator that is applied to two solutions χxi and χyj and
Πt+1 would be: mutation operators applied to χzk :
1) Regular Crossover: This crossover is the standard
π1 π2 π3 π4 π5 π6
crossover operator that can be a single point or a multiple
5 4 6 3 1 2
point crossover. The operator is applicable only if x = y. An
In general, a reversal ρti,j at index t in a solution will desig- example of this crossover is depicted in Figure 1.a.
nate two place indexes in the permutation where 1 ≤ i, j ≤ n 2) Absorption crossover: This crossover operator is appli-
specifying that the permutation in Π between i and j is to cable only if x 6= y. Without loss of generality let x < y,
be reversed to form Πt+1 . Let solution k of length m be a then in this process, i exchanges a subsequence with a random
sequence of reversals χm 1 2 3 m
k = hρ , ρ , ρ , . . . , ρ i, so if the subsequence of j of equal length. An example of this crossover
initial permutation is Π1 , then the permutation generated by is shown in Figure 1b.
solution k is Πk = Π1 · ρ1 · ρ2 · . . . · ρm . Let the number 3) Adjunction Crossover: This crossover operator generates
of breakpoints in solution k’s permutation Πk be B(Πk ) offspring that can be longer or shorter than their parents.
Therefore the two objectives of the search are to identify a It selects two random indexes in i and j then replaces a
solution , χm , where m is minimized and B(Π ) = 0. shorter sequence in one for a longer sequence in the other.

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Fig. 2. A sample run of the algorithm for a permutation with length 35,
showing the progression of the best individual of the population.
The selected index is chosen in a manner that enables the
algorithm to generate offspring longer than their parents. An
example of this crossover is depicted in Figure 1.c.
B. Modified Mutation
Our modified mutation operator probabilistically decreases
the length of an individual or changes some values of that
individual by applying standard mutation operator. Given an
individual solution, χzk = hρ1 , ρ2 , ρ3 , . . . , ρz i, the specialized
operator first chooses two random reversals ρi , ρj within that
individual i, j; i < j; i ≥ 1; j ≤ z. Let the indexes defining
the reversals for ρi be ha, bi and the indexes defining the
reversal for ρj be hc, di, then the new solution is formed by
removing b and c and shifting all intervening reversal indexes.
This operator effectively reduces the length of the solution by
one.
C. Complexity of Method
The complexity of the method can easily be determined.
The size of the population is maintained at n log n and the
number of algorithm iterations is fixed at n log n. It requires
on average O(m2 ) steps to evaluate each solution and log n
to select the next population then the complexity will be
O(n2 m2 log2 n). Given that we know m is bound by n, since
this is the maximum number of breakpoints a solution can
contain, the final complexity is given by: O(n4 log2 n).
III. E XPERIMENTS AND R ESULTS
We conducted experiments on different permutations to
compare the quality of solutions among competing heuristic
methods: the 3/2 algorithm introduced by [7] and a GA
approach described in [9]. For permutations with size lesser
or equal to approximately 110, our algorithm is effective
and finds a short series of reversals needed for sorting the
permutation. In this area, it outperforms both alternative algo-
rithms. For longer permutations, the algorithm can terminate
due to the imposed limit on iterations rather than identifying
the solution with no break points. These solutions can easily
be repaired to reduce the number of breakpoints to zero
by using the näive algorithm. In our experiments, size of
population and the number of generations are both n log n.
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Fig. 3. Quality of solutions found by the three methods for increasing size of
problem. Note that the method described here produces on average solutions
that are shorter by 20% than the 3/2 algorithm and on average 4% better than
the previous GA method.
The settings for the competing algorithms are the same as
stated in their references. A sample run for a permutation
with length 35 is depicted in Figure 2; this figure shows the
process of minimizing the first objective. The performance of
our proposed method for permutations with length lesser than
110 is compared with the two other methods in Figure 3.
IV. D ISCUSSION
Genome rearrangement is a challenging and important prob-
lem in bioinformatics. Inversions (reversals) are a common
occurrence in genome rearrangement and therefore an im-
portant question for biologists who want to understand how
species evolve from common ancestors, both under natural and
artificial selection. Biologists seek the solution that involves
the minimum number of genetic reversals, but there is no
intrinsic reason why this sequence would be the one that
actually occurred during evolution. However, the shortest
solution can provide the clearest interpretation of the process
and offers the chance for scientists to engineer mutations that
lead to specific traits in organisms. Since it is computationally
impossible to find this optimal solution, heuristic solutions
have been developed that find sub-optimal solutions whose
length is close to the minimum.
In this paper, we proposed a modified multi-objective based
genetic algorithm to solve this problem. The key idea in
the method is that the population contains individuals of
diverse lengths and genetic operators manipulate both the
length and the arrangement of reversal steps in the solution.
Two complementary objectives are employed during the search
process that measure both the actual length of the solution and
the estimated length of steps needed to complete the solution,
reminiscent of the A* method [10] used to find satisfying
solutions to many NP-hard problems.
A potential drawback of our method is its limit in solv-
ing long permutations problems. This deficiency could be
explained by the high correlation between the reversals within
individuals, which is a common problem in GA methods; the
longer the individual, the higher correlation between reversals
due to accumulated crossover operators. This weakness may be
overcome by specializing the operators further to exploit this
correlation so that common sub-sequences become schema in
the solutions and therefore accelerate problem solving. This
issue is left as an open research problem.
ACKNOWLEDGMENT
Authors thank Dr. Minghui Jiang at Utah State University
for his help in this research.
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