jMetalMSA is an Open source software tool aimed at solving multiple sequence alignment (MSA) problems by using multi-objective metaheuristics. It is based on the jMetal multi-objective framework, which is extended with an encoding for representing MSA solutions.

The object-oriented architecture of jMetalMSA is shown in Figure above, is composed of four core classes (Java interfaces). Three of them (MSAProblem, MSAAlgorithm, and MSASolution) inherits from their counterparts in jMetal (the inheritance relationships are omitted in the diagram), and there is a class Score to represent a given MSA scoring function.

##List of Algorithms The list of metaheuristics currently available in jMetalMSA include the evolutionary algorithms

• NSGA-II [1]
• NSGA-III [2]
• SMS-EMOA [3]
• SPEA2 [4]
• PAES [5]
• MOEA/D [6]
• MOCell [7]
• GWASF-GA [8].

The crossover operator is the Single-Point Crossover adapted to alignments, randomly selects a position from the parent A by splitting it into two blocks and the parent B is tailored so that the right piece can be joined to the left piece of the first parent (PA1) and vice versa. Selected blocks are crossed between these two parents

The list of mutation operators included in jMetalMSA are:

• Shift-closed gaps: Closed gaps are randomly chosen and shifted to another position.
• Non-gap group splitting: a non-gap group is selected randomly, and it is split into two groups.
• One gap insertion: Inserts a gap in a random position for each sequence.
• Two adjacent gap groups merging: Selects a random group of gaps and merge with its nearest group of gaps.
• Multiple mutation

The scores that are currently available in jMetalMSA are:

• Sum of Pairs
• Weighted Sum of Pairs with Affine Gaps
• Single sTRucture Induced Evaluation (STRIKE).
• Percentage of Totally Conserved Columns.
• Percentage of Non-Gaps

To use jMetalMSA the following software packages are required:

• Java SE Development Kit 8
• Apache Maven
• Git
• Strike Contacts Generator