gws_omix

🔍 Introduction

Multiple Sequence Alignment Visualizer is an automated tool designed to align and visualize biological sequences either protein or nucleotide by combining the MAFFT aligner with the pyMSAviz visualization library.

It provides:

• High-quality multiple sequence alignment (MSA) via MAFFT.
• Clean, publication ready alignment figures (PNG format).
• Automatic detection of DNA vs protein color schemes.

🧰 Prerequisites

• Access to Constellab and a valid Digital Lab environment
• Installed brick: gws_omix version ≥ X.X.X
• Input file: A FASTA file containing ≥ 2 sequences (either nucleotide or protein).

🧪 Use Case Steps

• Import your FASTA file into Constellab. The file can contain either nucleotide or protein sequences (minimum two sequences required).
• Link it to the Task: Multiple Sequence Alignment
• Configure Parameters:
• prefix: Output prefix (default: FASTA filename stem). max_seqs: Maximum number of sequences to keep (default: 500). align_if_needed: If enabled (default = true), runs MAFFT automatically if the input is not pre-aligned. threads Number of CPU threads to allocate for the alignment process (default: 8).
• Run the Task

📂 Output

📊 Example Use Cases

✅ Visualizing homologous gene families Easily compare the alignment of gene or protein variants.

✅ Creating publication-ready figures Generate clean and consistent MSA images for reports or manuscripts.