Progressive Aligner for Multiple Sequence Alignment (MSA)

Features

• Consensus sequence pairwise alignment (adapted Needleman-Wunsch) as profile-profile alignment technique
• Uses either Neighbour Joining to calculate a guiding tree which determines the order in which two profiles get aligned.
• Or newly calculated distances (using consensus sequences) between each profile to determine which profiles to align next.

Run the application:

Download the JAR file from the latest release. Navigate to the folder in which the JAR was saved in and run it with:

java -jar progressiveAligner.jar <arguments...>

Available Parameters

Parameter	Short Flag	Type	Required	Description	Default
--fastaPath	-fp	[s] String	Mandatory	Specifies the path to the FASTA file containing at least 2 sequences.	-
--matchScore	-ms	[i] Integer	Optional	Positive value of the match score.	4
--misMatchScore	-mms	[i] Integer	Optional	Positive value of the mismatch score.	2
--gapPenalty	-gp	[i] Integer	Optional	Positive value of the gap penalty.	1

Available Commands

Command	Short Flag	Description
Consensus	c	Uses newly computed distances between profiles, based on consensus sequences, to decide which profiles to align next.
NeighbourJoining	nj	Builds a guiding tree using the Neighbour Joining method to determine the order of profile-profile alignments.

Clone and work on the SourceCode:

1. Prerequisites

Ensure the following tools are installed:

• Java Development Kit (JDK): Version 11 or higher (21 recommended).
• Maven: To build and manage dependencies.
• Git: To clone the repository.

2. Clone the Repository

3. Build the Project

Use Maven to compile the code, run tests, and package the application:

mvn clean install

This will:

• Resolve dependencies.
• Compile the source code.
• Run unit tests (if applicable).
• Create a packaged JAR file in the target directory.