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Multiple Sequence Alignment and Visualization (MSAVis)

This tool performs multiple sequence alignment using MUSCLE, tailored for accurate alignment of protein and nucleic acid sequences.

Key Features

  • High accuracy: Progressive alignment strategy with accuracy surpassing ClustalW2 and T-Coffee
  • Fast processing: Optimized algorithms deliver 3–5× speedup over traditional tools
  • Smart optimization: Iterative refinement ensures optimal alignment quality
  • Broad compatibility: Supports protein, DNA, and RNA sequences

Visualization

  • Multiple color schemes: Professional palettes including Clustal, Taylor, Zappo, etc.
  • Flexible display options: Grid lines, consensus sequence, sequence sorting, and more
  • Custom range: Specify start/end positions for focused analysis
  • Smart wrapping: Custom line length and spacing to fit display needs
  • SVG output: High-quality vector graphics with lossless scaling and download

1. Input FASTA sequences (protein/nucleic acid; up to 100, ≤1 MB):

Sequence count:0

Character length:0

User Guide

Input Requirements

  • Format: Standard FASTA; each sequence starts with ">" followed by an identifier
  • Count: Supports 2–100 sequences; 3+ recommended for better alignment
  • Size: Total input ≤1 MB; each sequence ≤10,000 residues recommended
  • Characters: Automatically filters spaces and nonstandard characters; case-insensitive input
  • Type: Automatically detects protein, DNA, and RNA sequences

Parameters

Color Schemes
  • Clustal: Classic palette by amino acid chemistry
  • Taylor: Based on physicochemical properties
  • Zappo: Groups by side-chain properties
  • Hydrophobicity: Gradient by hydrophobicity strength
  • Nucleotide: Palette specialized for nucleic acids
Display Options
  • Show grid lines: Adds grids for easier position reference
  • Show consensus: Displays conservation statistics at the bottom
  • Sort sequences: Automatically sorts by similarity
  • Position range: Specify start and end positions
  • Wrapping: Control residues per line

Algorithm

MUSCLE uses a three-stage progressive strategy:
Stage 1: Fast distance estimation and guide tree construction
Stage 2: Progressive alignment to build the initial MSA
Stage 3: Iterative refinement to improve accuracy

References

Primary reference:
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research. 2004;32(5):1792-1797. DOI: 10.1093/nar/gkh340