FESTIVE CLOSURE

Festive Closure

The service will close down over the festive period. We aim to process any sequencing samples arriving before or on the first post of Friday 22nd of December. Any sequencing samples arriving after that will be stored and processed on our return (3rd January). For other sample types please contact us.

Resources | Sequencing | Software & Viewers

The sites listed below provide general information that customers and other visitors to this site may find interesting and/or useful. The sites are not intended to provide detailed trouble shooting or other support information for our customers. For trouble shooting and general help, please see our FAQs and Troubleshooting pages.

Disclaimer: Please note that we are not responsible for the content of any of these sites below and cannot take responsibility for them.

Chromatogram Viewers

Below are a selection of freeware and shareware applications for both Macintosh and PC 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

Viewers for MS Windows

Viewers for Linux

 

Viewers for Apple Macintosh

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.

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.

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.

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.

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 and Windows OS.

 

Viewers for MS Windows

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.

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.

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.

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.

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.

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 and Windows OS.

 

Viewers for Linux

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.

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!

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 and Windows OS.

Sequence Analysis Software

Below is a list of various programs that can be used to manipulate and analyse DNA and/or protein sequences. Applications for Macintosh and PC that allow you to perform downstream analysis on your DNA sequences. Some of these applications also allow you to view the chromatogram output.   

Please note that these programs will NOT allow you to "re-analyse" the sequence output you have received from us. This is only possible using PE Biosystems licenced software that we have.

Analysis software for Apple Macintosh

Analysis software for MS Windows

Analysis software for Linux

 

Analysis software for Apple Macintosh

CLC Free Workbench

As the name suggests, this is a free application (available in Windows, Mac OSX and Linux (RedHat and SuSE flavours)). It allows many types of data format to be imported into the application and then offers various DNA and protein analysis tools, including multiple sequence alignments.

DNADynamo

This is a cross-platform "Java" application and will run on Windows, Mac OSX and Linux computers. Apart from being able to view the chromatogram files, you can also edit the sequence, perform translations, do restriction digests, etc. You can even perform NCBI blast searches from inside the program and do multiple sequence alignments. A free demonstration version is available from the software developer (Blue Tractor Software) for evaluation purposes.

DNASTAR

DNASTAR produce the Lasergene suite of DNA manipulation programs for both PC and Macintosh. Apart from providing a range of DNA manipulation modules, this software is capable of directly reading PE Biosystems format sequence and displaying PE Biosystems electropherograms.

DNA Strider

This Macintosh-only application is a useful (and relatively cheap) program that performs most of the common manipulations that molecular biologists will need. It is possible to import sequences (in various formats, including the ASCII output from the PE Biosystems sequencers), then perform restriction mapping, translations, reverse complementing, etc. It is also possible to compare two DNA sequences. One slight quirk is the use of the character "*" to indicate an ambiguous base. Everyone else uses "N"! However, if you import a sequence containing "Ns", it will automatically convert them to "*s". In addition, it will analyse protein sequences and provide various predictions regarding secondary structure, etc. Various ways of comparing two protein sequences is also allowed. In short, if you are a molecular biologist and use a Macintosh computer, you can do a lot worse than invest in this program. To obtain this program please email Christian Marck (marck at jonas.saclay.cea.fr).

Macvector

This Macintosh program will perform the usual DNA/protein manipulations you would expect from such software (e.g. restriction enzyme analysis, primer pair design, sequence comparison). It also allows for on-line BLAST searches at NCBI (of course you could just use the NCBI BLAST server directly!).

Sequencher

This program is available in both Macintosh (OSX) and Windows versions and comes from Gene Codes Corporation. It provides tools for viewing, editing and assembling data generated by automated sequencers. One of the most powerful features of the software is its contig assembly function that allows multiple sequences to be alligned and a common contig sequence to be obtained. It is possible to download a demo version of the software from the web site.

 

Analysis software for MS Windows

DNassist

This a PC Shareware program that will do many of the things that more powerful (and expensive) programs will also do. If you are a molecular biologist with a limited budget and a need to perform the standard sorts of DNA manipulations that most molecular biologists do each day, give this program a go. It may be just the thing for you!

Sequencher

This program is available in both Macintosh (OSX) and Windows versions and comes from Gene Codes Corporation. It provides tools for viewing, editing and assembling data generated by automated sequencers. One of the most powerful features of the software is its contig assembly function that allows multiple sequences to be alligned and a common contig sequence to be obtained. It is possible to download a demo version of the software from the web site.

pDRAW32

This program is available for Windows and comes from AcaClone software. It provides tools for general DNA manipulation such as restriction digest maps, open reading frame identification, methylation site analysis, sequence editing, virtual gel image and (as the name suggests) generating nice plasmid maps. It also has a Tm calculator. This is free software.

 BioEdit

This program is available for Windows. It provides tools for viewing, editing and assembling data generated by automated sequencers. It also allows automated Blast searches, plasmid drawing and annotation, restriction mapping, translations, etc. It is free software and really is quite a comprehensive application for manipulating DNA and protein sequences.

CLC Free Workbench

As the name suggests, this is a free application (available in Windows, Mac OSX and Linux (RedHat and SuSE flavours)). It allows many types of data format to be imported into the application and then offers various DNA and protein analysis tools, including multiple sequence alignments.

DNADynamo

This is a cross-platform "Java" application and will run on Windows, Mac OSX and Linux computers. Apart from being able to view the chromatogram files, you can also edit the sequence, perform translations, do restriction digests, etc. You can even perform NCBI blast searches from inside the program and do multiple sequence alignments. A free demonstration version is available from the software developer (Blue Tractor Software) for evaluation purposes.

DNASTAR

DNASTAR produce the Lasergene suite of DNA manipulation programs for both PC and Macintosh. Apart from providing a range of DNA manipulation modules, this software is capable of directly reading PE Biosystems format sequence and displaying PE Biosystems electropherograms.

 

Analysis software for Linux

CLC Free Workbench

As the name suggests, this is a free application (available in Windows, Mac OSX and Linux (RedHat and SuSE flavours)). It allows many types of data format to be imported into the application and then offers various DNA and protein analysis tools, including multiple sequence alignments.

DNADynamo

This is a cross-platform "Java" application and will run on Windows, Mac OSX and Linux computers. Apart from being able to view the chromatogram files, you can also edit the sequence, perform translations, do restriction digests, etc. You can even perform NCBI blast searches from inside the program and do multiple sequence alignments. A free demonstration version is available from the software developer (Blue Tractor Software) for evaluation purposes.

Do you need any help? Please get in touch and we’ll be happy to lend a hand.