Tool
Annotation
Archived

SeqTools

A suite of tools for visualising sequence alignments

The SeqTools package contains three tools for visualising sequence alignments: Blixem, Dotter and Belvu.

Archive Page

This page is maintained as a historical record and is no longer being updated.

About

Blixem is an interactive browser of sequence alignments that have been stacked up in a “master-slave” multiple alignment; it is not a ‘true’ multiple alignment but a ‘one-to-many’ alignment. Dotter is a graphical dot-matrix program for detailed comparison of two sequences. Belvu is a multiple sequence alignment viewer and phylogenetic tool with an extensive set of user-configurable modes to color residues.

Supported platforms

Our primary supported platform is Ubuntu 14.04 (64-bit). SeqTools is well tested and in daily use on this architecture. It is also tested frequently on Mac OS X. It should also work on several other platforms, as listed below, but is less thoroughly supported.

  • Linux – Ubuntu 14.04 (64-bit) – primary supported architecture
  • Linux – other
  • Mac OS X (Intel)
  • Windows (under Cygwin)
  • Other platforms (using VirtualBox)
  • FreeBSD (in the ports).

Blixem features

  • Overview section showing the positions of genes and alignments around the alignment window
  • Detail section showing the actual alignment of protein or nucleotide sequences to the genomic DNA sequence.
  • View alignments against both strands of the reference sequence.
  • View sequences in nucleotide or protein mode; in protein mode, Blixem will display the three-frame translation of the reference sequence.
  • Residues are highlighted in different colours depending on whether they are an exact match, conserved substitution or mismatch.
  • Gapped alignments are supported, with insertions and deletions being highlighted in the match sequence.
  • Matches can be sorted and filtered.
  • SNPs and other variations can be highlighted in the reference sequence.
  • Poly(A) tails can be displayed and poly(A) signals highlighted in the reference sequence.

Dotter features

  • Every residue in one sequence is compared to every residue in the other, and a matrix of scores is calculated.
  • One sequence is plotted on the x-axis and the other on the y-axis.
  • Noise is filtered out so that alignments appear as diagonal lines.
  • Pairwise scores are averaged over a sliding window to make the score matrix more intelligible.
  • The averaged score matrix forms a three-dimensional landscape, with the two sequences in two dimensions and the height of the peaks in the third. This landscape is projected onto two dimensions using a grey-scale image – the darker grey of a peak, the higher the score is.
  • The contrast and threshold of the grey-scale image can be adjusted interactively, without having to recalculate the score matrix.
  • An Alignment Tool is provided to examine the sequence alignment that the grey-scale image represents.
  • Known high-scoring pairs can be loaded from a GFF file and overlaid onto the plot.
  • Gene models can be loaded from GFF and displayed alongside the relevant axis.
  • Compare a sequence against itself to find internal repeats.
  • Find overlaps between multiple sequences by making a dot-plot of all sequences versus themselves.
  • Run Dotter in batch mode to create large, time-consuming dot-plots as a background process.

Belvu features

  • View multiple sequence alignments.
  • Residues can be coloured by conservation, with user-configurable cutoffs and colours.
  • Residues can be coloured by residue type (user-configurable).
  • Colour schemes can be imported or exported.
  • Swissprot (or PIR) entries can be fetched by double clicking.
  • The position in the alignment can be easily tracked.
  • Manual deletion of rows and columns.
  • Automatic editing of rows and columns based on customisable criteria:
    • removal of all-gap columns;
    • removal of all gaps;
    • removal of redundant sequences;
    • removal of a column by a user-specified percentage of gaps;
    • filtering of sequences by percent identity;
    • removal of sequences by a user-specified percentage of gaps;
    • removal of partial sequences (those starting or ending with gaps); and
    • removal of columns by conservation (with user-specified upper/lower cutoffs).
  • The alignment can be saved in Stockholm, Selex, MSF or FASTA format.
  • Distance matrices between sequences can be generated using a variety of distance metrics.
  • Distance matrices can be imported or exported.
  • Phylogenetic trees can be constructed based on various distance-based tree reconstruction algorithms.
  • Trees can be saved in New Hampshire format.
  • Belvu can perform bootstrap phylogenetic reconstruction.

Software pipelines

As well as being used independently, Blixem, Dotter and Belvu can also be called from other tools as part of a software pipeline. A common workflow is to call Blixem from the ZMap genome browser to analyse a set of alignments in more detail, and to call Dotter from within Blixem to give a graphical representation of a particular alignment. Belvu has an extensive set of command-line arguments for specifying processing and output parameters, making it possible to perform complete processes in a single command-line call.

Background

Blixem, Dotter and Belvu were originally written as part of the AceDB genome database system. Version 4 of the programs involved an extensive re-write to take advantage of modern GUI toolkits and to separate them from AceDB to form this independent SeqTools package. They can be used independently or with any other tool that outputs data in a suitable format – the current preferred file formats are FASTA and GFF v3 for Blixem and Dotter; a variety of file formats are supported by Belvu.

Links

Downloads

Production release

This is the recommended release for most users. It is well-tested, stable and supported code.

Please download the latest version from the FTP site.

Development build

Reasonably stable development code, which contains most of the latest features.

Please download the latest version from the FTP site.

Daily build

Experimental code; not guaranteed to be stable (or even to compile). Should only be used if you require the very latest changes.

Please download the latest version from the FTP site.

Linux

  • Install the following pre-requisites. This is most easily done using your system package manager (e.g. synaptic on Ubuntu, available from the System/Administration menu). Depending on your system, packages may be named differently or additional packages may be required. In this case the ./configure step below will fail and you will need to install the required package before running it again. If you cannot find a package it can be useful to search for just the main part of the name excluding numbers/dashes, e.g. “gtk” or “libgtk” rather than “libgtk2.0-dev”.
libcurl4-gnutls-dev (optional)
libgtk2.0-dev
libglib2.0-dev
libreadline6-dev
libsqlite3-dev      (optional)
  • In the terminal, unpack the downloaded seqtools tar file using the following command, where XXX is the version you downloaded:
tar -xf seqtools-XXX.tar.gz
  • To install in the default location (usually /usr/bin):
cd seqtools-XXX
./configure
make
make install

To install in a different location, or for help with dependencies, see the tips section. For more detailed instructions, see the INSTALL file in the source code.

Mac OS X

  • Install the following pre-requisites. We strongly recommend that you use MacPorts to install these packages as this will also install any dependencies for you.
curl    (optional)
gtk2
glib2
sqlite3 (optional)
  • In the terminal, unpack the downloaded seqtools tar file using the following command, where XXX is the version you downloaded:
tar -xf seqtools-XXX.tar.gz
  • To install in the default location (usually /opt/local/bin):
cd seqtools-XXX
./configure
make
make install

To install in a different location, or for help with dependencies, see the tips section. For more detailed instructions, see the INSTALL file in the source code.

Windows / Other platforms

SeqTools cannot currently run natively on Windows. However, it can be installed and run in a virtual machine (VM) using VirtualBox. It should also be possible to install SeqTools using Cygwin (which provides a Linux-like environment on Windows). The VM uses more disk space and memory, but is likely to be more robust because it can emulate our primary supported architecture.

VirtualBox (all platforms)

  • Download and install VirtualBox.
  • Download the 64-bit Ubuntu 14.04 image.
  • Open VirtualBox and create a new VM, using the Ubuntu 14.04 image.
  • Start the VM and go through the Ubuntu installation procedure.
  • Install the guest additions (from the Devices menu, select “Insert Guest Additions CD image…”).
  • Restart the VM to apply the changes.
  • You should then be able to install SeqTools by following the standard Linux instructions above. You can type the following in a Terminal to install the pre-requisites:
sudo apt-get install libcurl4-gnutls-dev libgtk2.0-dev libglib2.0-dev libreadline6-dev libsqlite3-dev
  • More detailed instructions are available here.

Cygwin (Windows only)

  • From the Cygwin website , download setup-x86.exe (or setup-x86_64.exe if you have a 64-bit machine).
  • Run the setup program, accepting all the default options. You will need to choose a mirror on the Choose Download Site page (e.g. cygwin.mirror.constant.com).
  • On the Select Packages page, select these packages:
Devel/gcc-core
Devel/gcc-g++
Devel/libsqlite3-devel  (optional)
Devel/make
Devel/pkg-config
Editors/nano            (optional)
Libs/libcurl-devel      (optional)
Libs/libglib2.0-devel   **also tick SOURCE checkbox**
Libs/libgtk2.0-devel    **also tick SOURCE checkbox**
Libs/libreadline-devel  (or Libs/readline)
Web/wget                (optional)
X11/xinit
  • When installation is complete, open the Cygwin terminal and type the following commands, replacing XXX with the version of SeqTools you want to download:
wget
ftp://ftp.sanger.ac.uk/pub/resources/software/seqtools/PRODUCTION/seqtools-XXX.tar.gz
tar -xf seqtools-XXX.tar.gz
cd seqtools-XXX
./configure
make
make install
  • You need to start an “xterm” terminal to run the SeqTools programs from. This can be done
    by typing the following in the Cygwin terminal:
export DISPLAY=:0; startxwin -- -emulate3buttons &
  • Alternatively, to start the xterm automatically each time you open the Cygwin terminal,
    you can add the above command to your bash profile. To do this, type the following
    in the Cygwin terminal (you only need to do this once):
echo "DISPLAY=:0; startxwin -- -emulate3buttons &" >> ~/.bash_profile

For further help, see the tips section or the INSTALL file in the source code.

FreeBSD

Please see the ports page.

Tips

  • You may need to run make install using sudo if you do not have root privileges, i.e.:
sudo make install
  • Alternatively, to install to a different location (e.g. one not requiring root privileges), use the –prefix argument when you run ./configure. For example, the following command would set the install location to foo/bar in your home directory:
./configure --prefix=~/foo/bar
  • If GTK+ is not in the default location then you may need to pass its location to the configure script. GTK+ is usually installed in /usr/lib, /usr/local/lib, /opt/lib or /opt/local/lib. If GTK+ is in e.g. /opt/local/lib then you would call configure with the following arguments:
./configure PKG_CONFIG_PATH=/opt/local/lib/pkgconfig LDFLAGS="-Xlinker -rpath -Xlinker /opt/local/lib"

Further information

Getting started

Run the programs without arguments to see their usage information, or try out the examples given in the examples directory of the source-code download.

For more details, see the README file in the source code.

Help pages

Help pages, including a quick-start guide and user manual, are installed along with the programs. They can be accessed from within the programs using either the Help menu, the lifebuoy icon on the toolbar, or the Ctrl-H keyboard shortcut. They are included in the doc/User_doc directory in the source code..

User manuals

User manuals are installed along with the programs. The manuals for the current production versions can also be downloaded here:

Other documentation

Other documentation, such as design notes, is included in the doc directory in the source-code. It can also be viewed here.

SeqTools is free software and is distributed under the terms of the Apache Version 2.0 License.

SeqTools should be credited to “Genome Research Ltd”

External Contributor

Photo of Erik Sonnhammer

Erik Sonnhammer