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TOPALi has now been superceded by TOPALi v2.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)


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

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:

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