HAlign4

HAlign4 is a high-performance multiple sequence alignment software based on the star alignment strategy, designed for efficiently aligning large numbers of sequences. Compared to its predecessor HAlign3, HAlign4 further enhances the ability to handle long sequences and large-scale datasets, enabling fast and efficient alignment on standard computing devices.

Background

HAlign3 was implemented in Java and was capable of efficiently aligning ultra-large sets of similar DNA/RNA sequences, but had limitations when dealing with long sequences and very large datasets. To address these issues, HAlign4 was reimplemented in C++ and incorporates the Burrows-Wheeler Transform (BWT) and wavefront alignment algorithm.

Key Improvements

• Algorithm Optimization: Replaced the original suffix tree with BWT for more efficient indexing and searching.
• Memory and Speed Optimization: Introduced the wavefront alignment algorithm to reduce memory usage and improve alignment speed, especially for long sequences.

Installation Methods

1. Conda Installation

This method uses Conda to create an isolated environment and install HAlign4 with all dependencies.

conda create -n halign4
conda activate halign4
conda install -c malab halign4
halign4 -h

2. Source Installation with Make

This method allows you to manually compile HAlign4 using Make. For here to get lastest release.

Steps:

1. Install required packages:

   You need to have Make and a C++ compiler installed. On Ubuntu, you can install them as follows:

   sudo apt-get update
   sudo apt-get install gcc

2. Clone the repository:

   git clone --recursive https://github.com/metaphysicser/HAlign-4.git
   cd HAlign-4

3. Compile with Make:

   make

4. Run HAlign4:

   After the build process completes, the executable halign4 will be available in the current directory. You can run it using the following command:

   ./halign4 -h

Usage

By following either of these methods, you can successfully install and run HAlign4. Choose the method that best fits your development environment.

./halign4 Input_file Output_file [-r/--reference val] [-t/--threads val] [-sa/--sa val] [-h/--help]

Parameter Description

• Input_file: Path to the input file or folder (please use .fasta as the file suffix or input folder).
• Output_file: Path to the output file (please use .fasta as the file suffix).
• -r/--reference: Reference sequence name (please remove all whitespace), default is the longest sequence.
• -t/--threads: Number of threads to use, default is 1.
• -sa/--sa: Global sa threshold, default is 15.
• -h/--help: Show help information.

Example

Here is a simple example of using HAlign4 for multiple sequence alignment:

./halign4 input.fasta output.fasta -t 4

This command will use 4 threads to align the sequences in the input.fasta file, and the result will be saved in the output.fasta file.

License

HAlign4 is developed by the Malab team under the MIT License.