A simple and efficient C++ implementation of three classic sequence alignment algorithms:

• Longest Common Subsequence (LCS)
• Global Alignment (Needleman-Wunsch)
• Local Alignment (Smith-Waterman)

The alignments are visualized with colored base-level matches and mismatches for clarity.

Please refer to API Documentation

To use OpenMPI compilers (mpicc, mpic++, etc.) and mpirun on Fedora:

1. Install OpenMPI and development headers:

   sudo dnf install openmpi openmpi-devel

2. Enable environment modules:

   source /etc/profile.d/modules.sh

3. Load the OpenMPI module:

   module load mpi/openmpi-x86_64

NOTE: Sometimes, you need to run the above command before cmake and make commands.

4. Persistent setup (optional): Add the above two lines to your ~/.bashrc to avoid repeating them in each session.

Reference: OpenMPI on Fedora

Install OpenMPI and development files with:

sudo apt install libopenmpi-dev

Install using Homebrew:

brew install openmpi 
brew install llvm

For official documentation, see: OpenMPI Quickstart Guide

Each version implements the same interface. Choose the appropriate binary based on the features or optimizations you want to test.

For Debian/Ubuntu, Fedora, and the following commands will build the project:

git clone https://github.com/yourusername/SequenceAligner.git
cd SequenceAligner
mkdir build && cd build
cmake ..
make
cd ..

For macOS (Intel Chip), you can use the following commands:

git clone https://github.com/yourusername/SequenceAligner.git
cd SequenceAligner
mkdir build && cd build
cmake .. \
  -DCMAKE_C_COMPILER=/usr/local/opt/llvm/bin/clang \
  -DCMAKE_CXX_COMPILER=/usr/local/opt/llvm/bin/clang++ \
  -DCMAKE_C_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/llvm/include" \
  -DCMAKE_CXX_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/llvm/include" \
  -DCMAKE_EXE_LINKER_FLAGS="-L/usr/local/opt/llvm/lib -lomp"
make
cd ..

For macOS (Apple Silicon), you can use the following commands:

git clone https://github.com/yourusername/SequenceAligner.git
cd SequenceAligner
mkdir build && cd build
cmake .. \
  -DCMAKE_C_COMPILER=/opt/homebrew/opt/llvm/bin/clang \
  -DCMAKE_CXX_COMPILER=/opt/homebrew/opt/llvm/bin/clang++ \
  -DCMAKE_C_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/llvm/include" \
  -DCMAKE_CXX_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/llvm/include" \
  -DCMAKE_EXE_LINKER_FLAGS="-L/opt/homebrew/opt/llvm/lib -lomp"
make
cd ..

This will compile an executable named aligner in the project's directory:

• aligner → builds from src/main.cpp

To run on cluster or server with OpenMPI, use the following command:

mpirun -np <num_processes> ./aligner \
  --query <query.fasta> \
  --target <target.fasta> \
  --choice <1|2|3|4> \
  --mode <dna|protein> \
  [--outdir <output_directory>] \ 
  [--binary <binary file DP>] \ 
  [--txt <text file DP>] \
  [--gap_open <float>] \
  [--gap_extend <float>] \
  [--verbose]

Note: Use mpirun when you want performance via parallelism—especially for long sequences or many alignments.
It can run on multiple CPU cores or even multiple nodes if configured

To run on local machine, use the following command:

./aligner \
  --query <query.fasta> \
  --target <target.fasta> \
  --choice <1|2|3|4> \
  --mode <dna|protein> \
  [--outdir <output_directory>] \ 
  [--binary <binary file DP>] \ 
  [--txt <text file DP>] \
  [--gap_open <float>] \
  [--gap_extend <float>] \
  [--verbose]

The program accepts standard FASTA files.

This project was originally developed in 2014 as part of the Biological Computation course during my Bachelor's in Bioinformatics at JUIT, Solan. It was later revisited and optimized for better performance, readability, and maintainability.

This project is licensed under the BSD 3-Clause License
© 2025 Abhinav Mishra.