TOPALi

TOPALi provides an intuitive graphical interface for working with existing statistical methods designed for detecting recombination in DNA sequence alignments. Once recombinant regions have been identified, further (automated if desired) analysis is then possible, including the creation of Phylogenetic trees, mosaic structure predictions, and HTML report generation.

TOPALi has now been superceded by TOPALi v2. Click here for details.

Current version is 0.28, released 21st Nov 2005 (view changelog)

• Download TOPALi now

The following is a short list of some of the features and functionality TOPALi provides:

• Load DNA multiple alignments in a variety of commonly used formats
• Edit or prune alignments (manually or through phylogeny) to reduce dataset sizes
• View alignments with full user-definable colour-coding and scaling
• Run one of three statistical methods to detect recombination on alignments from 3 to n sequences in size
  • PDM (Probabilistic Divergence Measures) and Pruned PDM
  • HMM (Hidden Markov Models)
  • DSS (Difference of Sums of Squares)
• View results graphically and in real-time as they are generated (real-time results available with PDM and DSS only)
• Compare and overlay graphs from different runs, and interact with them to select alignment subsets and partitions
• Partition alignments manually or automatically via a result set's thresholds, then use those partitions to automatically predict the alignment's mosaic structure
• View the mosaic structure in full-colour, and modify its parameters to affect how it looks
• Create phylogenetic trees for the whole alignment, or just for sequence or partition subsets
• Export partitions, graphs, trees, and mosaic structure diagrams in a variety of formats (GIF, SVG, plain text, etc)
• Generate HTML reports that automatically run all of TOPALi's supported analysis methods for you

You can also view TOPALi's online help for more information on what is available.

TOPALi is written in (and requires) Java, and should work on any platform that supports Java 1.4.1 or later. Note however, that its analysis methods work by calling external C++ programs. These have currently been compiled and tested on Windows, Unix (Solaris) and Linux (RH 8 and 9 & Fedora). It may be possible to compile some or all of them (and hence use those methods within TOPALi) on other platforms, but we cannot offer any support for this as we have no way of testing this ourselves.

(TOPALi is released under the GNU General Public License. See here for further information on this and the licenses for TOPALi's helper applications).

Selected publications related to this work, include:

• Milne I, Wright F, Rowe G, Marshal DF, Husmeier D and McGuire G (2004), TOPALi: Software for Automatic Identification of Recombinant Sequences within DNA Multiple Alignments, Bioinformatics 20 (11), 1806-1807. View PDF.
  
• Husmeier D and McGuire G (2003), Detecting Recombination in 4-Taxa DNA Sequence Alignments with Bayesian Hidden Markov Models and Markov Chain Monte Carlo, Molecular Biology and Evolution 20 (3), 315-337.
• Husmeier D and Wright F (2001), Probabilistic Divergence Measures for Detecting Interspecies Recombination, Bioinformatics 17, Suppl. 1, S123-S131.
• McGuire G and Wright F (2000) TOPAL 2.0: Improved Detection of Mosaic Sequences within Multiple Alignments, Bioinformatics, 16 (2), 130-134.

Please do not hesitate to contact us at topali (at) bioss.ac.uk if you have any further queries or comments about this software.