Merge Alignments

Combine multiple sequence alignments into a single aligned file for phylogenetic and comparative analysis.

Alignment Statistics

Sequences
0
Total Length
0
Alignment 1
0
Alignment 2
0

What is Merge Alignments?

This tool concatenates multiple sequence alignments horizontally, maintaining the alignment structure. Essential for combining gene alignments for phylogenetic analysis and creating super-matrices.

How to Use This Tool

  1. Paste first alignment in FASTA format
  2. Paste second alignment with matching sequence names
  3. Select merge options (separator, gap removal)
  4. Download the concatenated alignment

When to Use

  • Creating concatenated gene alignments
  • Building super-matrices for phylogenetics
  • Combining protein domain alignments
  • Merging aligned genomic regions

Example Alignments

>Seq1
ATCG--AT
>Seq2
AT--CGAT

Both alignments must have the same sequence names.

Merge Options

Separator: Adds "NNN" between alignments

Remove gaps: Removes columns with only gaps

Check names: Ensures matching sequences

FAQ

Q: What if sequences don't match?
A: The tool will show a warning and skip mismatched sequences.

Q: Can I merge more than 2 alignments?
A: Merge two at a time, then merge the result with the next.