Color Align Conservation accepts a group of aligned sequences (in FASTA or GDE format) and colors the alignment. The program examines each residue and compares it to the other residues in the same column. Residues that are identical among the sequences are given a black background, and those that are similar among the sequences are given a gray background. The remaining residues receive a white background. You can specify the percentage of residues that must be identical and similar for the coloring to be applied. Use Color Align Conservation to enhance the output of sequence alignment programs.

Paste the aligned sequences in FASTA or GDE format into the text area below. Input limit is 20000 characters.

  • Show residues per line.
  • Percentage of sequences that must agree for identity or similarity coloring to be added:
Enter the groups of similar amino acids separated by commas to be used for the similarity calculation. If you are coloring a DNA alignment, leave this text area empty.

Enter the starting positions of the sequences separated by commas (to alter residue numbering). An example entry is: 0, 200, 0, 0. If no numbers are given, the default starting position of 0 is used for each sequence.


P. Stothard. The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 2000; 28: 1102, 1104.