1. 2.1  download and setup
    1. 2.1.1    complete setup file (including excel.exe)
    2. 2.1.2    seqtools core setup file
    3. 2.1.3    older versions of seqtools
    4. 2.1.4    registration and license
  2. 2.2  auxiliary components
    1. 2.2.1    clustal
    2. 2.2.2    blastall, formatdb, bl2seq, blastclust, fastacmd
    3. 2.2.3    blastcl3
    4. 2.2.4    entrez
    5. 2.2.5    convert_trace
    6. 2.2.6    chromas
    7. 2.2.7    t-coffee
  3. 2.3  emboss components
    1. 2.3.1    fuzznuc, fuzzpro, fuzztran
    2. 2.3.2    merger
  4. 2.4  interfaced programs
    1. 2.4.1    how to associate external programs to seqtools
    2. 2.4.2    genedoc
    3. 2.4.3    treeview
    4. 2.4.4    chromas
  5. 2.5  verify the current SEQtools installation
    1. 2.5.1    installed components
    2. 2.5.2    updating seqtools and external components
    3. 2.5.3    install/update external programs from seqtools
    4. 2.5.4    install/update external programs manually
    5. 2.5.5    license and registration
    6. 2.5.6    importing old seqtools data
  6. 2.6  testing Internet access
  7. 2.7  system requirements
    1. 2.7.1    computer
    2. 2.7.2    dual monitor display
  8. 2.8  about firewalls

2.1 download and setup seqtools ver. 8.3

2.1.1 Complete setup file (including excel.exe)

The complete setup file, seqtools83ex.msi, contains in addition to the basic SEQtools application and the auxiliary and emboss components, ms excel. After downloading the installation file (approximately 15 Mb) double-click the seqtools83ex.msi file to install SEQtools.

2.1.2 Seqtools core setup file

The core SEQtools setup file seqtools83.msi contains all files necessary to install SEQtools application without spreadsheet support (ms excel not included). After downloading the setup file (approximately 10 Mb) double-click the seqtools83.msi file to run the installation program.

2.1.3 Older versions of Seqtools

Seqtools is developed and tested on Windows 2000 and Windows XP operating systems. Users not using either of these operating systems may not be able to run SEQtools versions 8.2 or 8.3.

Version 8.0 of SEQtools can be installed using, seqtools80.msi (8.0.804) and 8.2 using seqtools82c.msi (8.2.094).

Note, however, that none of these version are supported. You are of course welcome to contact me in case you run into problems but do not expect too much...

2.1.4 Registration and license

When you install SEQtools for the first time you automatically get a students license which is valid for 60 days. When the students license expires you can extend the license for a new 60 days period by renewing the registration (version 8.0 and 8.2 only). You can continue renewing your license for as long as you wish. Using ver. 8.3 requires a full license.

Note, however, that you cannot upgrade beyond the version number covered by your license. In case you wish to upgrade to a newer version of SEQtools you must first get a new license - even if the 60 day period has not yet expired. You can read more about about registration and licenses on theregistration page.

2.2 auxiliary components

If you wish to update functions depending on NCBI support, trace file processing and viewing and the functions using emboss programs, you can do this by downloading the self-extracting auxiliary8.exe and emboss8.exe files and install the components from the SEQtools Help/SEQtools Configuration menu as describedbelow.

The auxiliary8.exe file contains the following programs:

2.2.1 Clustal

...is 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. 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.

2.2.2 Blastall, Formatdb, bl2seq, Blastclust, Fastacmd

...are required for a number of tasks all depending on this collection of utilities made available by NCBI. The tasks include creating and searching local databases with the five blast programs, comparing sequences, performing batch blast searches at Genebank etc. The current version of the NCBI programs is 2.2.11.

2.2.3 Blastcl3

...is 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.

2.2.4 Entrez

...is required for retrieval of sequence records and Medline entries from Entrez

2.2.5 Convert_trace

...is required to extract and import chromatograms generated by the most common auto-sequencers. In addition to convert_trace, the two dll's: read.dll and zlib.dll are necessary for this function. Convert_trace is part of the Staden package.

2.2.6 Chromas

...is 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.

2.2.7 t-Coffee

...is 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.

2.3 emboss programs

The fourEmbossprograms interfaced with SEQtools are Windows versions of selected programs from the Emboss package. The programs are from the distribution made available by André Blavier and include version 2.7.1-0.7, September 2004 of the package.

2.3.1 Fuzznuc, Fuzzpro, Fuzztran

...are required for nucleic acid pattern search, protein pattern search and protein pattern search after translation - respectively.

2.3.2 Merger

...is required for merging two overlapping nucleotide sequences.

2.4 interfaced programs

2.4.1 How to associate external programs to seqtools

To associate a 3rd party program to SEQtools open Preferences/General Preferences/Launch Application, place the cursor on the first empty line of the list, click Browse to find the location of the program you wish to associate and click Enter to include the application in the list. As described below GeneDoc and TreeView communicate directly with SEQtools while other programs just opens when their name on the Launch menu is clicked.

2.4.2 GeneDoc


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 theGeneDochomepage, run the setup file and tell SEQtools where to find the genedoc exe-file as described above.

2.4.3 TreeView

TreeViewis a simple program for displaying phylogenies on Windows PCs. It has the following features:

  1. - reads many different tree file formats (including NEXUS, PHYLIP, Hennig86, NONA, MEGA, and ClustalW/X)
  2. - supports standard the TrueType and Postscript fonts
  3. - supports native graphics file format (Windows metafile) for copying and saving
  4. - print preview
  5. - can print multiple trees per page, and one tree over more than one page
  6. - has drag-and-drop facility for easy opeing of files
  7. - includes access toWeb-based online help
  8. - includes facilities forediting trees

To make TreeView available to SEQtools download the program from theTreeViewhomepage, run the setup file and tell SEQtools where to find the exe-file as described above.

2.4.4 Chromas

The interaction between SEQtools and Chromas is entirely handled by SEQtools and does not require that Chromas is included in the Launch menu as described above unless of course you wish to have direct access to this application outside the SEQtools control.


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.

2.5 verify installation

2.5.1 Installed components

This form, Help/SEQtools Configuration lists currently installed auxiliary and emboss components and their file dates. Installed external supported are listed in the lower part of the form. If items are missing they can be downloaded and installed by clicking the "UPDATE now..." fields of the form.

2.5.2 Updating seqtools and external components

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 Help/SEQtools Configuration. You have to exit and restart SEQtools in order to install the updates when downloading is completed.

To manually update SEQtools or one of the auxiliary components simply click the relevant UPDATE now... field on the form. Look at thedownload pageon the web for more details.

2.5.3 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 the relevant UPDATE now...field to download and install auxiliary (or emboss) programs.

2.5.4 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:

2.5.5 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.

2.5.6 Importing old SEQtools data

In case you want SEQtools to search for existing data and components on your hard disk from a previous installation, simply click the import user data field. This will start a search/import facility copying old data to your current data folders, default location: c:\windows folder\ST8_TEMP\

2.6 internet access

When SEQtools loads it checks whether or not a live connection to the Internet can be detected. This check involves an attempt to connect to the URL specified in the form shown below. The default URL is www.google.com but can be altered if you prefer a different URL.

2.7 system requirements

2.7.1 Computer

Seqtools is designed to run on 32bit Windows based PC's and it is not possible to run the program on Macs, Unix, Linux and other non-Windows operating systems. However, according to some users SEQtools runs fine under Virtual PC on Macintosh.

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 2.8 Ghz Pentium IV equipped with 2 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.

2.7.2 Dual monitor display

With a large number of forms SEQtools benefits from computers set up to use two monitors. It is a major advantage when analysing sequences with SEQtools to split the tasks on two separate monitors. Both Win2000 and WindowsXP operating systems handle this smoothly without requiring additional drivers - except an extra screen card.

2.8 firewalls

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. TheNCBI blastcl3 helpfilemay be helpful in setting up the communication between SEQtools and NCBI programs through a firewall.

  © 2002-2010S.W. Rasmussen  (revised: )