Biomathematics & Statistics Scotland


December 2021: Please note that TOPALi web services are now End of Life and unavailable. You can still run TOPALi analyses locally by CTRL/CMD clicking on the Run button.

Statistical and evolutionary analysis of multiple sequence alignments

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.

Nov 2008: We now have a new TOPALi publication in Bioinformatics:
TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops

"Version 2" of TOPALi is a complete overhaul to the original TOPALi. Analyses methods that used to run locally within TOPALi can now optionally run remotely on high-performance compute clusters.

Current version is 2.5 (build 13.04.03), released 3rd April 2013 (view changelog)

Download TOPALi v2 now

TOPALi Screenshot TOPALi Screenshot

Please do not hesitate to contact us at 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 was funded by the BBSRC.