Alignment Quality Scorer

What is Alignment Quality Scorer?

Alignment Quality Scorer is a bioinformatics tool that assesses multiple sequence alignment quality using various computational metrics. It calculates sum-of-pairs scores, column conservation rates, gap penalties, and overall alignment quality scores. These metrics help validate alignment reliability before downstream analyses like phylogenetic tree construction or comparative genomics studies.

How to Use This Quality Scorer

Quick guide to assess alignment quality:

1. Paste or upload your multiple sequence alignment in FASTA format
2. View calculated quality metrics automatically in the results panel
3. Assess alignment quality based on conservation and gap scores
4. Refine or trim alignment if scores indicate poor quality
5. Download metrics report for documentation

When to Use Quality Scorer

This tool is essential when you need to:

• Validate alignment quality before phylogenetic analysis
• Compare different alignment algorithms or parameters
• Identify poorly aligned regions that need manual curation
• Assess whether alignment requires trimming or refinement
• Document alignment quality for publication or reporting

Example Input

Sample multiple sequence alignment:

Alignment in FASTA format with gaps marked as '-'.

Example Output

Quality metrics displayed:

Scores help determine if alignment is suitable for analysis.

FAQ

Q: What is a good quality score?
A: Above 80 is excellent, 60-80 is good, below 60 may need refinement or trimming.

Q: What alignment formats are supported?
A: FASTA format with gaps marked as dashes (-) or dots (.).

Q: How do I improve a low-quality alignment?
A: Try using alignment trimmer, adjusting alignment parameters, or removing problematic sequences.