This Python script processes FASTA files to ensure that all sequences have the same length by padding shorter sequences with gaps ("-") and trimming longer sequences. It identifies the longest sequence in the file as the reference length and adjusts all other sequences accordingly. This normalization is crucial for bioinformatics analyses, such as phylogenetic tree construction and multiple sequence alignment, where input sequences must be uniform in length.

This script is useful in a variety of bioinformatics applications:

• Phylogenetic Tree Construction: Ensures sequences are of equal length for tree-building tools like IQ-TREE and RAxML.
• Multiple Sequence Alignment (MSA): Prepares sequence data for tools like MAFFT and ClustalW, which require consistent sequence lengths.
• Molecular Evolution Analysis: Supports tools like PAML and BEAST that analyze genetic variation, conserved regions, and selection pressure.
• High-Throughput Data Processing: Normalizes large genomic datasets, ensuring compatibility with online platforms and local software.
• Error Handling for Online Tools: Prevents job failures due to sequence length issues in servers like IQ-TREE.
• Educational Tool: Ideal for teaching sequence alignment and bioinformatics data preprocessing.

1. Automatic Length Adjustment: Detects the longest sequence and adjusts all others to match.
2. Error Handling: Improves robustness by managing incomplete or improperly formatted sequences.
3. Easy Integration: Simple to run or integrate into bioinformatics pipelines.

• Python 3.6 or higher
• Libraries:
  • biopython for parsing and processing FASTA files

This script is ideal for bioinformaticians and researchers working with sequence data in evolutionary, molecular, and genomic studies. It ensures compatibility with tools like IQ-TREE and other alignment or phylogenetic software, making it an essential part of the bioinformatics data preprocessing pipeline.