WARNING: Se-Al will not run on Mac OS X 10.7

Due to the lack of support for older PPC code (via the 'Rosetta' system present in older versions). Do not upgrade to Lion 10.7 if you wish to continue using Se-Al. It may be possible to run 10.6 (Snow Leopard) in a virtual machine but I have yet to get this to work.

Se-Al is an application for creating multiple sequence alignments from nucleotide and amino acid sequences. At the moment it does not do any automatic alignments but is intended for the production of hand alignments and for preparing input for alignment programs such as CLUSTAL and phylogeny reconstruction programs such as PHYLIP and PAUP. It is particularly useful for manipulating protein coding DNA/RNA sequences.


  • The import and export of sequences in a range of commonly used formats. At the moment, NEXUS, PHYLIP, MEGA, NBRF, FASTA, GDE and GDE flat formats are supported. Some of these formats are unreliable either because the format is not well defined or I couldn't be bothered. Email me with files that fail to import.
  • For nucleotide sequences of protein-coding genes the user can freely switch between three mode: nucleotides - edit the alignment at the level of single bases, codons - edit the alignment of codons in any reading frame, and translation - edit the alignment of the infered amino acids translated using various genetic codes (editing done in this mode is actually done to the original nucleotide sequences allowing alignment of amino acids but the export of the final alignment as nucleotide). Shifting reading frames, reversing and complementation can all be done independantly to any sequence and undone.
  • Alignments can be edited by selecting a block of sequences and sliding it relative to the other sequences. Gaps will open up behind the block. These changes can be undone.
  • Sequences and their labels can be edited in a separate window. Raw sequences can also be pasted from other sources (such as GENBANK text files and email) into this window. Spaces, formating and non-sequence characters (e.g. numbers) are automatically removed.
  • A consensus sequence can be displayed above the alignment.
  • Alignments are saved in a binary format allowing rapid opening and the conservation of any transformations (i.e. reading frames, complementation or translation) that have been used.
  • Cut, Copy and Paste whole sequences or sections of alignment within and between alignment documents. Copy and paste between Se-Al and other applications in Nexus format.
  • Drag and Drop sequences, alignments and regions between windows or to other applications in Nexus format.
  • Search for motif or region similar to a given sequence (very primitive at the moment).

The following features are still to be implemented:

  • More formats for the import and export of sequences, If there is demand for a particular format then I will try and include it.
  • Search for best alignment of sequence pairs.
  • Run user-created AppleScripts or Java Applets from menu.
  • A range of analysis functions.
To run on older Mac OS (v8.6-9.2) please
download and install this Apple library (CarbonLib 1.6)

Version History

2002-08-08 - v2.0a11

Fixes a few bugs
New features:
  • Can now write in an XML-based format
Bugs fixed:
  • Improved reading of Genbank files.
  • Fixed problem reading Se-Al files containing empty sequences.
  • Improved reading of PHYLIP files.
  • Miscellaneous fixes.
Andrew Rambaut, 2007