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Bioinformatics Institute


Squint v1.02 - Multiple Sequence Alignment Editor

Squint is an advanced alignment tool. It brings together algorithmic alignment of molecular sequences, with human editing. It is an extension of the alignment editor available in Pebble. The easy to use and powerful interface provides the following features:

  • Import/export sequence/alignment data in a number of formates (Fasta/Nexus/Clustal/Phylip).
  • Edit the placement of the gaps in an alignment, with the option of two views of the data being edited (with one view showing the data as DNA, the other as amino acid for example).
  • Dynamic feedback on the effect of changes to the alignment on one or more measures of alignment score.
  • Realign either all the sequences, or just a selected area of the total alignment.
  • Perform alignments based on a format different from that of sequences, and have the results mapped back to the orginal data. For example, align a nucleotide sequence by amino acid or codon.


OS Support

Squint is written using the Java programming language. As such it is relatively cross-platform independent. Versions are provided for Windows, Linux and MacOS.


Squint is provided as is, with no warranty. The developers, the Bioinformatics Institute, The University of Auckland, and any other associated parties, provide no warranty for the use of Squint. While every effort is taken to provide a reliable and trustworthy application, the authors, and associated parties, accept no liability for any damages, loss, or inconvenience caused by the use of Squint.

Install Squint

Windows and Mac OS X:

Click on the appropriate link below to run the installer.


Right-click on the appropriate link, select "Save Link As..." and save the installer in a convenient place. After downloading open a commandline shell and go to the directory where you saved the installer.
To run the installer, at the prompt type: sh ./


Windows Download (2.8Mb)
Mac OS X Download (2.3Mb)
Linux/Unix Download (2.3 MB)
Sample data file ( Download (24kb)