ataserinyelMSA 0.1.0

A simple MAFFT-based Multiple Sequence Alignment (MSA) library

ataserinyelMSA

A simple MAFFT-inspired Multiple Sequence Alignment (MSA) tool written in Python.

Installation

pip install ataserinyelMSA

Usage

python main.py input.fasta output.fasta

Example

Input (input.fasta):

>seq1
GATTACA
>seq2
GCATGCU
>seq3
AGCTAGC

Output (output.fasta):

>seq1
-GAT-TACA
>seq2
-GC-ATGCU
>seq3
AGCTA-GC-

Algorithm

This tool implements a simplified version of the MAFFT FFT-NS-1 algorithm:

1. FASTA Parsing - Read and write FASTA format files
2. Pairwise Alignment - Needleman-Wunsch global alignment algorithm
3. Distance Matrix - Compute pairwise distances between sequences
4. Guide Tree - UPGMA clustering algorithm
5. Progressive Alignment - Align sequences following the guide tree order

Differences from original MAFFT

• Uses Needleman-Wunsch instead of FFT for similarity calculation
• Simple +1/-1 scoring matrix instead of advanced substitution matrices
• Suitable for small datasets

Author

Ata Serinyel