SEQTOOLS 8.4 - Standard / Education / Students Edition
Download and run the Windows installation file seqtools84.msi (does not include excel.exe)
or seqtools84ex.msi (if you do not already have Excel installed on your PC) to install
For teaching purposes version 8.4 can be run with a limited selection of functions available. This
makes the user interface much simpler. This option is intended for class room teaching
hiding the more complex functions for the students while allowing the teacher to have access
to the full version of the program. Type a lower case 's' while seqtools is loading to launch
the limited version of the program.
SEQtools 8.4 downloads seqtools v. 8.4.071 *) seqtools84.msi 15.316 mb seqtools v. 8.4.071 (with excel.exe) *) seqtools84_ex.msi 20.042 mb auxiliary components - 01.05.2007 auxiliary8.exe 8.084 mb emboss components - 24.03.2007 emboss8.exe 0.933 mb nucleotide sample sequences nucleotide_sample.exe 0.864 mb
*) Please note that the update from v. 8.4.066 to v. 18.104.22.168 does not include any changes of
the functions contained in Seqtools but only handles various problems associated with running
the program on Windows 7 32/64 bit computers. If your copy of Seqtools works without
problems there is no reason to update to v. 8.4.071.
When you install the program you have a 60 days trial period. Then you have two options:
All users have access to the same, updated full version of seqtools 8.4.
- You can either apply for an extension of the free students license which allows you
to continue using seqtools for another 60 days period. You can continue extending
the free students license for as long as you wish.
- Or you can invest in a full license which does not require continued renewal, never
expires and entitles you to full technical support.
To assist me in covering the expenses of maintaining the program, senior scientists are
encouraged to invest in a full license, while students are welcome to use seqtools free
This liberal license policy rests on the philosophy that senior scientists - like myself - have
a responsibility to assist younger people in their efforts to establish themselves in the
The price of a single-user full license to seqtools is € 29.00 - with significant discounts
when buying multi-user licenses. You can purchase your full license by visiting the seqtools
on-line payment page.
Soeren W. Rasmussen, December 4. 2012
The installation of seqtools is described below.
seqtools setup file
The setup file contains everything you need to run seqtools. After downloading the setup file double-click the self-extracting zip-file which contains the installation file *.msi. Then run the installation program to setup seqtools.
If you wish to update the functions depending on NCBI support, trace file processing and viewing and the functions using emboss programs, self-extracting auxiliary8.exe and emboss8.exe files can be downloaded separately and installed as described below.
third party programs
Seqtools communicates directly with three independent applications described below, GeneDocfor editing and annotating multi-sequence alignments, TreeViewfor building phylogenetic trees and Chromas for viewinf chromatograms.
To make the these applications available to seqtools install the programs on your PC and use general preferences in seqtools to create links between seqtools and the two of the three programs by including them in the seqtools launch menu. The third one, Chromas, is automatically installed and recognised by seqtools as part of the auxiliary components.
about registration and license
When you install seqtools for the first time you automatically get a license which is valid for 60 days. When this expires you can extend the students license for a new 60 days period by renewing the registration (seqtools 8.2 only) - or get a full license which does not require renewal (versions 8.2 and 8.4).
You can continue renewing your license for seqtools 8.2 for as long as you wish whereas version 8.4 requires a full license after the 60 days trial period.
You can read more about about registration and licenses on theregistration page.
self-extracting update files contains the latest versions of the executable, the help file, restriction enzyme files and the genbank database list for updating an existing installation of seqtools.
Seqtools looks for new updates when you start the program and notifies you if an update is available. New updates can be downloaded and installed from the seqtools configuration menu located under the main help menu. You have to exit and restart seqtools in order to install the update when downloading is completed.
If the automatic update facility fails you can download the self-extracting update file yourself and replace the existing seqtools files with the new ones.
license and registration
WARNING - Replacing your current version of seqtools with an update not covered by your license will cause seqtools to stop working. In this event, use theregistration formto get a new registration key allowing you to use the update.
To give you an impression of how seqtools handles nucleotide sequences you can download an annotated multi-sequence file, n_sample8.exe. To use the sample files, decompress the file and load the multi-sequence file into seqtools.
Several of the functions contained in seqtools require that the two selfextracting packages: auxiliary8 (contains different NCBI programs) and emboss8 (win32 versions of programs belonging to theemboss suite)are properly installed/updated to allow seqtools functions to communicate with them.
install/update external programs from seqtools
After installing seqtools start the program and click Help/seqtools Configuration... to display the the current configuration of seqtools. Then simply click update auxiliary (or update emboss) to download and install auxiliary (or emboss) programs.
install/update external programs manually
If this fails (for example because you are behind a firewall) it is possible to carry out the installation/updating of auxiliary8 and emboss8 programs manually:
- download the auxiliary8.exe and emboss8.exe files from the seqtools download page.
- after downloading to a temp folder unzip both files accepting the default destination, "c:\~seqtools\", suggested by winzip.
- start seqtools and accept to install auxiliary and emboss files from a local folder.
firewall and NCBI access
If you are behind a firewall read the informationbelowabout setting up your local server permissions to enable the NCBI programs in auxiliary8 to communicate with the Blast and Entrez servers at NCBI.
the auxiliary file includes...
- clustal - required for multi-sequence alignment. ClustalX is a stand-alone program launched from seqtools with the selected sequences as parameters. ClustalW is a command line DOS program entirely controlled by the seqtools user interface. The clustalx/w exe files and the clustal help file must be present in the main seqtools directory to allow seqtools to activate the multi-sequence alignment function. Version 1.83 of clustalx/w is included in the auxiliary file available for downloading. The clustal programs were written by:
Toby Gibson EMBL, Heidelberg, Germany.
Des Higgins UCC, Cork, Ireland.
Julie Thompson IGBMC, Strasbourg, France.
Francois Jeanmougin IGBMC, Strasbourg, France.
- muscle - required for multi-sequence alignment.See theMuscle websitefor more details.
- blastall, formatdb, bl2seq, blastclust, fastacmd - required for setting up seqtools for creating and searching local databases with the five blast programs and for comparing sequences. The exe-files as well as the files contained in the data directory are all included in the auxiliary file. Current version of the NCBI programs is 2.2.15 released October 2006
- blastcl3 - required for database searching on Genbank databases at NCBI. In some cases there may be a problem if you are behind a firewall. Consult the NCBI blastcl3helpfileand/or your system administrator for advice.
- entrez - required for retrieval of sequence records and Medline entries from Entrez
- convert_trace - required to extract and import chromatograms generated by the most common auto-sequencers. In addition to convert_trace, the two dll's: read and zlib are necessary for this function. Convert_trace is part of the Staden package.
- chromas - required for viewing chromatogram files. Note that versions of chromas earlier than 162 are freeware whilst newer versions require registration and a license fee. Read more about chromas on thechromaswebsite.
- t-coffee - required for optimisation of sequence alignments generated by clustalw. Note that t-coffee is extremely greedy with respect to RAM resources. If the amount of free RAM is insufficient t-coffee stalls and fails to optimise the alignment. The auxiliary file contains version 1.37 of t-coffee. Read more about t-coffee on thet-coffeewebsite. Note that seqtools includes an older version of t-coffee compiled for Windows.
the emboss file includes...
To enable data transfer between seqtools and the third party programs,
install the programs from their setup files. Then, in seqtools use the Launch option
include the applications in the seqtools launch menu.
This establishes the link between seqtools and the external program.
GeneDoc is a powerful editor which allows you to manually edit and add a wide range of attributes to multi-sequence alignments generated by Clustal W.
To make GeneDoc available to seqtools download the program from theGeneDoc homepage and run the setup file.
TreeView is a simple program for displaying phylogenies on Windows PCs. It has the following features:
- reads many different tree file formats (including NEXUS, PHYLIP, Hennig86, NONA, MEGA, and ClustalW/X)
- supports standard the TrueType and Postscript fonts
- supports native graphics file format (Windows metafile) for copying pictures into other applications, and for saving graphics files
- print preview
- can print multiple trees per page, and one tree over more than one page
- has drag-and-drop facility for easy opeing of files
- includes access toWeb-based online help
- includes facilities forediting trees
To make TreeView available to seqtools download the program from theTreeView homepage and run the setup file.
Chromas version 223 is included in the auxiliary8.exe file and the data transfer between seqtools and Chromas is automatically established when the auxiliary programs are installed. Visit theChromashomepage to read more about the program.
Updated restriction enzyme data files can be downloaded fromReBase. In addition to enzyme data files, the ReBase homepage contains a very useful search function which allows you to search their data base with the name of an enzyme or with a recognition pattern. Visit theReBasehomepage to download the restriction enzyme data file in GCG format.
how do I convert a gcg data file to seqtools format?
Seqtools uses a slightly different enzyme data file format so it is necessary to use the Convert GCG Data Files function under the Utilities menu to change the format so that the data file can be used with seqtools.
Seqtools is designed to run on 32bit Windows based PC's and it is not possible to run the program on Macs, Unix and other non-Windows operating systems.
Obviously the program runs more efficiently the more powerful the computer is. A
Pentium3 600 Mhz with 256 Mb RAM works well for small projects, i.e., 1-500 sequences
each of 500 bp. If you intend to work with larger projects, it is a good idea to add
more RAM to your PC. Currently we are using a dual processor 1.8 Ghz Pentium IV equipped
with 1 Gb RAM.
If you have problems running seqtools on your PC, let me try to help you. Write anemailwith as many details as possible describing the nature of the problem.
According to some users seqtools runs fine under Virtual PC on Macintosh.
Firewalls installed on local servers may in some cases prevent seqtools from communicating
with external resources such as the NCBI blast server.
While I will try to assist you as much as I can, it often turns out that such problems are very difficult to solve. The NCBI blastcl3helpfilemay be helpful in setting up the communication between seqtools and NCBI programs through a firewall.