There are a growing number of biological questions that can be answered by analysing multiple sequence alignment data. We have extended the original TOPALi Java application, beyond recombination detection, to launch a range of statistical and evolutionary analyses of multiple sequence alignments as web services. The extended TOPALi v2 provides phylogenetic model selection, Bayesian analysis (BA) and Maximum Likelihood (ML) phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis.
"Version 2" of TOPALi is a complete overhaul to the original TOPALi. Analyses methods that used to run locally within TOPALi now run remotely on high-performance compute clusters.
Current version is 2.5 (build 08.05.22), released 22nd May 2008 (view changelog)
TOPALi is released under the GNU General Public License and is available for most platforms supporting Java 1.5.x or higher. We strongly suggest you read over our privacy policy before using TOPALi.
Selected publications related to this work, include:
- Husmeier D, Wright F and Milne I (2005), Detecting interspecific recombination with a pruned probabilistic divergence measure, Bioinformatics, 21, pp 1797-1806.
- 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 help@topali.org if you have any further queries or comments about this software.
TOPALi was programmed by Iain Milne and Dominik Lindner. Its analysis methods contain code from Dirk Husmeier, Gràinne McGuire, and Adriano Werhli. The TOPALi project is managed by Frank Wright and is funded by the BBSRC.
