ABI Viewers

In order to open and view the ABI chromatogram files we now provide for downloading from our server, you must install a program on your computer that will allow you to do that. There are a few freeware programs, for both Mac and PC, which you can download from the Internet that will allow you to view, edit and print your color trace files. In addition, there are numerous commercial software packages that will allow you to open the ABI files and usually provide many more options such as alignment, contig building, potential open reading frames, etc. If you receive files from our 3100 and wish to open them on a Macintosh computer, you must first convert them so they are readable on the Mac. Go to the Applied Biosystems link:
http://www.appliedbiosystems.com/support/software/3100/conversion.cfm to download their free conversion utility.
Here is a list of a few of the free ABI viewing programs and their links and you can choose which one you like the best. We've included the company descriptions as well so you can see quickly what each package offers.

For RPCI, UB and HWI users: Now available through the Bioinformatics Resources at CCR are a number of DNA sequence analysis programs, including the Vector NTI Suite 8 and GCG packages, and usage of these programs is free to registered members. In addition, they have many useful links to publicly available analysis tools. Go to their website at: http://www.ccr.buffalo.edu/ for further information on how to register and access this software.

Freeware

For PC computers:

NEW! FinchTV: This is a really nice freeware program that has some neat features such as being able to select multiple panes in the page setup for printing your chromatogram; reverse and complement your chromatogram sequence; and zoom up and down on peaks for closer inspection.

Geospiza’s FinchTV is the popular way to view DNA sequence traces on Linux, Mac OSX, Windows, and Solaris. FinchTV started as the only chromatogram viewer that can display an entire trace in a scalable multipane view. Now it leads again with raw data views, BLAST searching and the ability to reverse complement sequences and traces.

The link to FinchTV is: http://www.geospiza.com/finchtv/

Chromas: This program has both freeware and shareware versions, and both are intuitive and easy to use. The freeware version allows you the basic options of opening, editing and printing the ABI files. The shareware version, which costs about $45.00, has the following features:

  • Current Version: 2.23
  • Opens chromatogram files from Applied Biosystems and Amersham MegaBace DNA sequencers.
  • Opens SCF format chromatogram files created by ALF, Li-Cor, Visible Genetics OpenGene, Beckman CEQ 2000XL and CEQ 8000, and other sequencers.
  • Save in SCF or Applied Biosystems format.
  • Prints chromatogram with options to zoom or fit to one page.
  • Exports sequences in plaint text, formatted with base numbering, FASTA, EMBL, GenBank or GCG formats.
  • Copy the sequence to the clipboard in plain text or FASTA format for pasting into other applications.
  • Export sequences from batches of chromatogram files, with automatic removal of vector sequence.
  • Reverse & complement the sequence and chromatogram.
  • Search for sequences by exact matching or optimal alignment.
  • Display translations in 3 frames along with the sequence.
  • Copy an image of a chromatogram section for pasting into documents or presentations.

The link to the freeware version is: http://www.technelysium.com.au/chromas14x.html
The link to order the shareware version or access the trial version is: http://www.technelysium.com.au/index.html

BioEdit: BioEdit is a biological sequence alignment editor written for Windows 95/98/NT. A rich, intuitive multiple document interface with many convenient features makes alignment, manipulation and viewing of sequences relatively quick and easy on your desktop computer. Several sequence manipulation and analysis options and fully-automated links to local and WWW-based analysis programs facilitate an integrated working environment which allows you to view, align and analyze sequences from a single application with simple point-and-click operations.

The link to BioEdit is: http://www.mbio.ncsu.edu/BioEdit/bioedit.html


GeneStudio: this company provides a program called SeqVerter which can be run as a stand-alone program, or can be downloaded as part of a 60-day free trial of their full molecular biology suite, GeneStudio Pro. SeqVerter allows you to do the following:

  • Open sequences from multiple source files simultaneously
  • View sequences
  • Select a subset of sequences for conversion
  • Select a subset of sequences for conversion
  • Merge sequences from different source files into one multiple sequence file
  • Split sequences from multiple sequence files into individual (single) sequence files
  • Trim ends of automatic sequencer-generated files
  • Merge sequences from different source files into one multiple sequence file
  • Enter file headers required by the GenBank sequence submission and update tool, SequIn.
  • Flush ends of alignment files
  • Compress alignments (delete empty columns)
  • Delete alignment columns containing nonstandard characters (e.g., unresolved bases)?BR>* Easily remove a single species (sequence) or several species from the alignment and from the analysis

The link to the SeqVerter stand-alone package is: http://www.genestudio.com/download_seq.htm
The link to the 60-day trial version is: http://www.genestudio.com/download_gspro.htm


TraceViewer: this package is a Java program available through CodonCode in conjunction with their commercial Phred-Phrap package. TraceViewer, on its own, is available to academic users for free. If you choose to process your ABI files with Phred, you can see your basecalling quality scores displayed when using TraceViewer to open your chromatograms. Features of TraceViewer include:

  • Read sequence traces from ABI or SCF files.
  • Display traces on white or black background.
  • Display Phred quality values as bars or numbers with one of three different color schemes.
  • Available for Windows, Macintosh, and Unix computers.
  • TraceViewer is free for academic users.

The link to TraceViewer software is: http://www.codoncode.com/TraceViewer/

For Mac computers:

EditView: this software is available from Applied Biosystems, manufacturers of our sequencers, and provides the basic options for viewing, editing and printing their files on a Macintosh. If you have received files from the PC-based 3100, don? forget to convert the PC files to Mac before opening them in EditView.

The link to EditView is: http://www.appliedbiosystems.com/support/software/dnaseq/installs.cfm

TraceViewer: this package is a Java program available through CodonCode in conjunction with their commercial Phred-Phrap package. TraceViewer, on its own, is available to academic users for free. If you choose to process your ABI files with Phred , you can see your basecalling quality scores displayed when using TraceViewer to open your chromatograms. Features of TraceViewer include:

  • Read sequence traces from ABI or SCF files.
  • Display traces on white or black background.
  • Display Phred quality values as bars or numbers with one of three different color schemes.
  • Available for Windows, Macintosh, and Unix computers.
  • TraceViewer is free for academic users.

The link to TraceViewer software is: http://www.codoncode.com/TraceViewer/