ReAlign-P: A vertical iterative realignment method for protein multiple sequence alignment

ReAlign-P is a tool written in C++17 for realigning the protein multiple sequence alignment. It runs on Linux.

🔨Installation and Usage

1.1 Linux/WSL(Windows Subsystem for Linux ) - from Anaconda

1.Install WSL for Windows. Instructional video 1 or 2 (Copyright belongs to the original work).

2.Download and install Anaconda. Download Anaconda for different systems here. Instructional video of anaconda installation 1 or 2 (Copyright belongs to the original work).

3.Install ReAlign-P.

#1 Create and activate a conda environment for ReAlign-P
conda create -n realign_p_env
conda activate realign_p_env

#2 Add channels to conda
conda config --add channels malab

#3 Install ReAlign-P
conda install -c malab realign_p

#4 Test ReAlign-P
realign_p -h

1.2 Linux/WSL(Windows Subsystem for Linux ) - from the source code

1.Download and Compile the source code. (Make sure your version of gcc >= 9.4.0)

#1 Download
git clone https://github.com/malabz/ReAlign-P.git

#2 Open the folder
cd ReAlign-P

#3 Compile
make

#4 Test ReAlign-P
./realign_p -h

2.Install the required alignment tools mafft and muscle5, we recommend using Conda to install.

# 1 Create and activate a conda environment for msa
conda create -n msa
conda activate msa
# 2 Install mafft and muscle
conda install -c bioconda mafft muscle=5.2

2 Usage

Usage: ./realign_p -i <input_file> [-o <output_file>] [-s <score_matrix>] [-l <length>] [-m <msa>]

Options:
  -i <input_file>    (required) Path to the input file containing sequence data.
  -o <output_file>   (optional) Path to the output file for storing results. Default is 'realign_p_result.fasta'.
  -s <score_matrix>   (optional) Score matrix to use, options are 'blosum62' or 'pam250'. Default is blosum62.
  -m <msa>           (optional) MSA tool to use, options are 'mafft' or 'muscle5'. Default is 'muscle5'.

Examples:
  ./realign_p -i data.fasta -o results.fasta -s pam250 -m mafft
  ./realign_p -i data.fasta -m muscle5

Note:
  - The '-i' option is required.
  - The '-m' option only supports 'mafft', and 'muscle5'.

🔬Test dataset and the use case

1. Information about the test dataset

Dataset	Nummber	Avg Number	Avg Length
BAliBASE	386	28.71	338.28
OXBench	395	8.33	138.58
PREFAB4	1682	45.19	233.51
SABRE	423	5.72	171.22

📍Reminder

1. Currently ReAlign-P is ONLY available for Protein.
2. Please ensure that the sequence ID entered into ReAlign is unique.
3. MAFFT and MUSCLE5 installation are required for the utilization of ReAlign-P.

🖥️Environment

System	GCC version
Linux	GCC 9.4.0
WSL	GCC 9.4.0

🙏References & Acknowledgements

We would like to acknowledge the following msa tools that contributed to the development of ReAlign-P:

• MAFFT: This is a widely used multiple sequence alignment tool known for its high accuracy and scalability.

• MUSCLE5: This is a novel algorithm which constructs an ensemble of high-accuracy alignment with diverse biases by perturbing a hidden Markov model and permuting its guide tree.

🔖Citation

👋Contacts

The software tools are developed and maintained by 🧑‍🏫ZOU's lab.

If you find any bug, welcome to contact us on the issues page or email us at 👉📩.

More tools and infomation can visit our github.