FMAlign2: A novel fast multiple nucleotide sequence alignment method for ultra-long datasets

FMAlign2 is a novel multiple sequence alignment algorithm based on FMAlign. It is designed to efficiently align ultra-long nucleotide sequences fast and accurately.

Table of Contents

• Installation
• Usage
• Data
• Issue
• Related
• Citation
• License

Installation

The program is supported both on Linux and Windows(Linux is strongly recommended for its convenience and better performance). Please make sure your computer meets the following requirements:

• To compile the executable program for the entire project, please ensure that you have the make command available.

  • Verify make availability: Open your command-line interface and type make --version to check if the make command is installed on your system. If it is installed, you will see the version information. If not, you need to install it before proceeding.
  • Install make on Windows: If you are using Windows, you may need to install the appropriate tool to enable make functionality. One popular option is GNU Make for Windows , which provides a Windows-compatible version of make. You can download it from the official website and follow the installation instructions.

• To compile the project, you need to have the g++ compiler available on your system. Here are the steps to ensure g++ support:

  • Check g++ availability: Open your command-line interface and type g++ --version to check if the g++ command is installed. If it is installed, you will see the version information. If not, you need to install it before proceeding.

  • Install g++ on Windows: If you are using Windows, you can install g++ by using a compiler suite such as MinGW or Cygwin. These packages provide a Windows-compatible version of g++ along with other essential tools. You can download MinGW from the official website (https://mingw-w64.org/) or Cygwin from their official website (https://www.cygwin.com/). Follow the installation instructions provided by the respective package to set up g++ on your system.

  • Install g++ on Linux: On most Linux distributions, the g++ compiler is included as part of the GNU Compiler Collection (GCC). To install g++, open your terminal and run the following command:

    sudo apt-get install g++
    

    This will install g++ and its dependencies on your system.

  • Verify g++ installation: After installation, run g++ --version again to verify that g++ is installed correctly and accessible from the command line. Please note that if you are a Windows user, make sure that the installed version(>4.2) of g++ supports OpenMP. On Windows systems, we utilize OpenMP for parallel computing.

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If you have ensured that your system meets the requirements mentioned above, you can proceed with the following steps to compile the executable file. However, you also have the option to directly use the pre-compiled executable file available in the Release.

1. DownLoad

   git clone https://github.com/metaphysicser/FMAlign2.git
   cd FMAlign2
   # for Linux
   chmod 777 ./ext/mafft/linux/usr/libexec/mafft/disttbfast

2. Build

   cd FMAlign2 && make [M64=1]

   Switch to the FMAlign2 directory in your terminal and execute the above command to build the project. We provide two compilation modes: 32-bit and 64-bit. In most cases, the 32-bit mode is sufficient to handle most data. However, if the concatenated length of all sequences exceeds the range of uint32_t (4294967295), you should add the M64 parameter when compiling the program to generate a 64-bit executable.

   • If you don't need the 64-bit mode, simply execute the make command.
   • If you need the 64-bit mode, execute the make M64=1 command.

   During the compilation process, please be patient as the time required depends on the size and complexity of the project.

   Once the compilation is complete, you will find the generated executable file in the specified output directory.

   Note: If you want to remove all the generated .o files, you can execute the following command:

   make clean

   This command will clean up the intermediate object files and leave only the source code and executable file in the project directory. Use this command when you want to start a fresh build or clean up unnecessary files to save disk space.

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Please note that if you choose halign2 and halign3 as your multiple sequence alignment methods, make sure you have Java environment installed. To check the version of Java installed on your system, you can open a command prompt or terminal and execute the following command:

java -version

This will display the installed Java version information.

If you don't have Java installed or if the installed version is not compatible, you can follow these steps to install Java:

To install Java on Windows:

1. Visit the official Java website at java.com or the OpenJDK website at openjdk.java.net.
2. Download the appropriate Java Development Kit (JDK) for Windows.
3. Run the downloaded installer and follow the on-screen instructions to complete the installation.
4. After the installation is complete, open a new Command Prompt and run java -version to verify that Java is installed and the correct version is displayed.

To install Java on Linux:

1. Update Package Lists: Run the command sudo apt update to update the package lists on your system.
2. Install OpenJDK: Run the command sudo apt install default-jdk to install the default version of OpenJDK.
3. Verify Installation: After the installation is complete, run java -version to verify that Java is installed and the correct version is displayed.

Once you have Java installed and verified the version, you should be able to use halign2 and halign3 for multiple sequence alignment.

Usage

Reminder: Please ensure that all external files (such as MAFFT, HALIGN, etc.) are properly copied to their corresponding directories. Pay close attention to the relative paths between FMAlign2 and the ext folder to avoid issues during execution,

if you are Linux user:

./FMAlign2 -i /path/to/data [other options]

if you are Windows user:

./FMAlign2.exe -i /path/to/data [other options]

if you want to show the parameters details:

./FMAlign2 -h

Parameters Details:

• -i [file path] [required] The path to the input file.
• -o [output path] [default: ouput.fmaligned2.fasta] The path to the output file.
• -p [package] [default: mafft] The MSA method used in parallel align. for example, halign3, halign2 and mafft.
• -t [int] [default: cpu number] The maximum number of threads that the program runs, the recommended setting is the number of CPUs.
• -l [int] [default: square root of mean length] The minimum length of MEMs, the default value is square root of mean length.
• -c [float] [default: 1] A floating-point parameter that specifies the minimum coverage across all sequences, with values ranging from 0 to 1.
• -f [mode] [default: global or local] The filter MEMs mode. The default setting is that if sequence number less 100, accurate mode otherwise global mode.
• -d [int] [default:0] Depth of recursion, you could ignore it.
• -v [int] [default:1] Verbose option, 0 or 1. You could ignore it.
• -h [help] print help information

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We will demonstrate with the example data mt1x.fasta, assuming you are running on a Linux system.

./FMAlign2 -i ./data/mt1x.fasta -l 20 -c 1 -p mafft -f gloabl -o output.fmaligned2.fasta

This command specifies the following options:

• Input data: mt1x.fasta located in the data folder.
• Minimum length of MEMs: 20.
• Sequence coverage of MEMs: 1.
• Parallel alignment method: mafft
• Alignment mode: global mode.
• Output file: output.fmaligned2.fasta will be generated in the FMAlign2 directory.

After running this command, you will obtain the aligned output in the output.fmaligned2.fasta file.

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If you want to evaluate the generated alignment results, you can run the sp.py script (requires a Python environment) with the following parameters:

python sp.py --input output.fmalign2.fasta --match 0 --mismatch 1 --gap1 2 --gap2 2

This command will calculate and print the SP (Sum-of-Pairs) score for the multiple sequence alignment results. The --input parameter specifies the input alignment file (output.fmalign2.fasta in this case), and the --match, --mismatch, --gap1, and --gap2 parameters define the scoring scheme for matches, mismatches, and gap penalties.

By running this command, you will obtain the SP score, which provides an evaluation of the alignment quality.

Data

Data can be assessed in data fold. All the data is compressed using xz compression. Before using it, please decompress the files.

Here are the methods to decompress the files on different operating systems:

Decompressing on Linux:

1. Open the terminal.

2. Navigate to the directory where the compressed file is located.

3. Run the following command to decompress the file:

   xz -d filename.xz
   

   Replace filename.xz with the name of the file you want to decompress.

Decompressing on Windows:

1. Download and install an xz compression tool for Windows, such as 7-Zip or WinRAR.
2. Right-click on the compressed file.
3. Select "Extract to" or a similar option to decompress the file.

Please note that the decompressed files will occupy more disk space. Make sure you have enough disk space to store the uncompressed files.

If you need more data, you can visit http://lab.malab.cn/~cjt/MSA/datasets.html for more datasets.

Issue

FMAlign2 is supported by ZOU's Lab. If you have any suggestions or feedback, we encourage you to provide them through the issue page on the project's repository. You can also reach out via email to zpl010720@gmail.com.

We value your input and appreciate your contribution to improving the project. Thank you for taking the time to provide feedback, and we will address your concerns as soon as possible.

Related

• FMAlign: a fast multiple nucleotide sequence alignment method based on FM-index
• HAlign3 and HAlign2
• WMSA and WMSA2
• TPRA: A refinement tool for ensembling different multiple sequence alignment results
• MSATOOLS: Some tools for MSA, like SP score, Q score and so on.

Citation

Pinglu Zhang, Huan Liu, Yanming Wei, Yixiao Zhai, Qinzhong Tian, Quan Zou, FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasets, Bioinformatics, 2024;, btae014, https://doi.org/10.1093/bioinformatics/btae014

License

Apache 2.0 © [MALABZ_UESTC Pinglu Zhang]