Chromatogram Viewers

General

Below are a selection of freeware and shareware applications that are available for viewing and editing the chromatogram output from our DNA sequencers. We strongly recommend that customers make use of such applications, since they can be very useful when attempting to resolve ambiguities within sequences or when trouble-shooting problems.

Viewers for Apple Macintosh

OSX badge 4Peaks

This application has been written to run natively on OSX and makes full use of the OSX interface. The application has lots of features and is more than just a "chromatogram viewer". The best feature is the application is totally FREE! The same people have other OSX applications that might be useful for scientists and are also free. We use this viewer ourselves.

OSX badge FinchTV

This is a multi-platform application and has lots of really advanced features like displaying quality scores, editing and saving edits, searching for patterns, printing in multiple formats and much more. What is more, the application is FREE! The current version is 1.4.

windows icon CodonCode Aligner

This is a Java program that allows the reading of sequence traces from ABI or SCF files, the display of traces on white or black background and the display of Phred quality values as bars or numbers with one of three different color schemes. CodonCode Aligner is a commercial application.

mac OS icon Traceviewer

This is a Java program that runs in the classic environment and allows the reading of sequence traces from ABI or SCF files, the display of traces on white or black background and the display of Phred quality values as bars or numbers with one of three different color schemes. TraceViewer is free for academic users.

mac OS icon Editview

This free application from Applied Biosystems will allow you to view, edit and print the chromatogram files on your Macintosh computer (it will run on almost any 68K or PowerPC Macintosh computer running classic mac OS). You can also export your sequence data in various file formats for use in downstream applications.

Note: There is a problem viewing some chromatogram files produced on our new 3730 DNA sequencer using Editview. This problem is known to ABI, but it seems unlikely that they will fix it. The problem manifests itself as a blank window with no chromatogram trace (the sequence is still visible). Clicking and dragging in the window causes the chromatogram to appear, but only while that portion of the chromatogram is visible. Users who experience this problem might prefer to use "Traceviewer".

Viewers for MS Windows

windows icon Chromas

This application will allow PC users to display, edit and print Applied Biosystems chromatogram files. You can even translate the sequence and reverse complement it! The current version of Chromas is 2.33 and this is a shareware application. There is also a freeware version called Chromas Lite.

windows icon CodonCode Aligner

This is a Java program that allows the reading of sequence traces from ABI or SCF files, the display of traces on white or black background and the display of Phred quality values as bars or numbers with one of three different color schemes. CodonCode Aligner is a commercial application.

windows icon BioEdit

This is a freeware program that many enjoy using. It can work with proteins & nucleic acids (including .ab1 files) to do alignments, editing and more... As with the "4Peaks" application mentioned above, it is much more than just a chromatogram viewer. Well worth considering. However, please note that if your sequencing reaction has failed (ie you have simply "NNNNN"), BioEdit will not open the file and instead displays an error.

windows icon FinchTV

This is a multi-platform application and has lots of really advanced features like displaying quality scores, editing and saving edits, searching for patterns, printing in multiple formats and much more. What is more, the application is FREE! The current version is 1.4.

Viewers for Linux

linux icon Traceviewer

This is a Java program that allows the reading of sequence traces from ABI or SCF files, the display of traces on white or black background and the display of Phred quality values as bars or numbers with one of three different color schemes. TraceViewer is free for academic users.

linux icon FinchTV

This is a multi-platform application and has lots of really advanced features like displaying quality scores, editing and saving edits, searching for patterns, printing in multiple formats and much more. What is more, the application is FREE!

linux icon ABIview

ABIview is part of the open source suite of applications called EMBOSS (European Molecular Biology Open Software Suite). This is a suite of applications developed and maintained by EMBL (the European Molecular Biology Laboratory). It has lots of features. The EMBOSS software also runs on Mac OSX.