Requirements

Se-Al v2.0 requires a PowerMac running MacOS 9.0 or better. It will run on MacOS 8.5 and later if CarbonLib 1.0.4 is installed. This is a library that can be obtained from the Apple website.

Version 1.0 requirments: Se-Al v1.0 should run on any Apple Macintosh computer with at least the following specifications: 68020 processor or better, System 7.0 or later, 2MB of memory (on top of that used by the operating system).

Description

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.

Features

• 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.

Older Version History:

Version 2.0a7b Released 11th June 2001.

I made a mistake compiling version 2.0a7 so that it was unable to open existing Se-Al files. This version corrects this problem. Other than that it is the same as version 2.0a7.

Version 2.0a7 Released 1st June 2001.

New features:

• New preferences -
  • General: Can choose to default to elasticated sliding or not (either way, the opposite behaviour can be obtained by holding option whilst sliding.
  • Export: Can choose a default file format for exporting (or set it to use whatever format was last imported. Can also select a default filename extension and file creator for each export format.
• If you import a file into an empty window, that file's name becomes the name of the window (without the extension if recognised).
• Can now read GCG's rich sequence format (.rsf) files.
• Can now select one of the sequence fields as "Sequence Info" in the Export dialog box. This is used when appropriate (PIR files) or added as a comment to Nexus format files.

Bugs fixed:

• Some problems with reading and writing PIR files.

Version 2.0a6 Released 30th May 2001.

Bugs fixed:

• Fixed problem cutting or deleting gaps at the end of sequences.
• Fixed problem with preferences becoming corrupted. If you have problems running Se-Al try dragging "System Folder:Preferences:Se-Al Preferences" to the trash. It would probably be best to do this anyway if you have altered the preferences. If you have created colour schemes already, load the old version of Se-Al and drag them to the desktop. You should be able to drag them back again in the new version.
• Fixed a problem dragging colour schemes from the preferences dialog box to the desktop (which creates a clipping file) and back again. You can now use this feature to store and swap colour schemes.

Version 2.0a5 Released 15th May 2001.

New features:

• Consensus sequence display (select 'Show Consensus' from 'Alignment' menu).
• More export file formats (PIR/NBRF, ClustalW, FASTA, GDE flat).
• User definable colour schemes for nucleotides and amino acids (set in Preferences). Inspector Window with information about alignment and sequences. Selected from the menu options or a button in the alignment window).
• Export dialog has been simplified (the other options were not available in the previous version). A new feature for flagging sites on or off will be added soon which will then allow gap stripping and the like that was previously only available when exporting an alignment.

Bugs fixed:

• Problem with corrupted ends of sequences when saving, exporting or aligning.
• Unspecified sequence type when pasting sequences in.
• Various crashing-type bugs when slide-aligning.
• Ruler going awry when slide-aligning.

Version 2.0a3

The first new version of Se-Al for about 4 years. Version 2.0 is a complete rewrite with many new features. It can handle sequences of any length (within the limits of your computer's memory), Note, however, that not all the features from Se-Al v1.0 are fully implemented yet (or working properly). Se-Al v2.0 can read files from Se-Al v1.0 but not the otherway round.