Alignment Trimmer

Remove gaps and poorly aligned regions from multiple sequence alignments with adjustable thresholds

Gap Threshold50%

Remove columns with gaps above this percentage

Conservation Threshold30%

Keep columns with conservation above this percentage

What is Alignment Trimmer?

Alignment Trimmer is a bioinformatics tool that removes gaps and poorly aligned regions from multiple sequence alignments. Based on TrimAl methodology, it uses adjustable gap and conservation thresholds to clean alignments before phylogenetic analysis. This improves tree construction accuracy by removing unreliable regions that could introduce errors into evolutionary inference.

How to Use This Alignment Trimmer

Quick guide to trim alignments:

  1. Paste or upload your multiple sequence alignment in FASTA format
  2. Adjust gap threshold slider (percentage of gaps to remove columns)
  3. Adjust conservation threshold slider (minimum conservation to keep columns)
  4. View trimmed alignment automatically in the output panel
  5. Download or copy the cleaned alignment

When to Use Alignment Trimmer

This tool is essential when you need to:

  • Prepare alignments for phylogenetic tree construction
  • Remove unreliable or poorly aligned sequence regions
  • Clean alignments with high gap content
  • Improve signal-to-noise ratio in evolutionary analysis
  • Standardize alignment quality for comparative studies

Example Input

>seq1 ATGCATGC----AT >seq2 ATGC----GCGCAT >seq3 ATGCATGCGC--AT

Example Output (50% gap)

>seq1 ATGCATGCAT >seq2 ATGCGCGCAT >seq3 ATGCATGCAT

Columns with >50% gaps removed

FAQ

Q: When should I trim my alignment?
A: Before phylogenetic analysis to remove unreliable regions that could introduce errors.

Q: What threshold should I use?
A: Start with 50% gap threshold, adjust based on alignment quality and dataset size.

Q: Will trimming affect my analysis?
A: Yes - proper trimming usually improves phylogenetic tree accuracy by removing noise.