MelihMSA

Create a bioinformatics tool using Python that helps researchers align multiple DNA sequences efficiently. Your application, named 'SeqAligner', will utilize the MelihMSA package, which is based on the MAFFT algorithm for sequence alignment. This tool will allow users to upload multiple FASTA formatted files containing DNA sequences and perform pairwise or multiple sequence alignments.

Step-by-Step Instructions:
1. Begin by setting up your Python environment and installing necessary packages including MelihMSA.
2. Design a user-friendly interface where users can upload their FASTA files.
3. Implement functionality within your application to process these files and extract DNA sequences.
4. Utilize MelihMSA to perform sequence alignment on these extracted sequences.
5. Display the aligned sequences back to the user in a readable format.
6. Add features such as saving the aligned sequences into new FASTA files for further analysis.
7. Consider adding options for different alignment methods provided by MelihMSA for customization.
8. Ensure the application can handle large datasets efficiently without crashing.

Suggested Features:
- User authentication for saving alignment results and sharing them with colleagues.
- Option to choose between different alignment algorithms supported by MelihMSA.
- Visualization of the alignment process and results through graphical representations.
- Integration with popular bioinformatics databases for direct sequence retrieval.
- Detailed documentation and tutorials for new users.

How MelihMSA is Utilized:
- Import MelihMSA at the beginning of your script and use its functions to read sequences from FASTA files.
- Call the appropriate MelihMSA function to perform the alignment based on user preferences.
- Use MelihMSA's output handling capabilities to manage and display the results effectively.