Clann¶
Description¶
The program Clann has been developed to provide implementations of several methods to construct supertrees and explore the underlying phylogenomic information from partially overlapping datasets. The methods implemented all allow the investigation of data in a phylogenomic context. It is important that the user understands the advantages and limitations of these methods. It is also important for the user to know that the software is designed to perform a number of different tasks, however the interpretation of the results is left entirely to the user.
Environment Modules¶
Run module spider clann to find out what environment modules are available for this application.
Environment Variables¶
- HPC_CLANN_DIR - installation directory
- HPC_CLANN_DOC - documentation directory
- HPC_CLANN_EXE - examples directory
Citation¶
If you publish research that uses clann you have to cite it as follows, depending on the methods used:
- Creevey, C. J., & McInerney, J. O. (2005). Clann: Investigating phylogenetic information through supertree analyses. Bioinformatics, 21(3), 390–392. https://doi.org/10.1093/bioinformatics/bti020
The Bootstrapping and YAPTP methods and the DFIT (most similar supertree algorithm) have all been described in the paper:
- Creevey, C. J., Fitzpatrick, D. A., Philip, G. A., Kinsella, R. J., O’Connell, M. J., Travers, S. A., Wilkinson, M., & McInerney, J. O. (2004). Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proceedings of the Royal Society B: Biological Sciences, 271(1557), 2551–2558. https://doi.org/10.1098/rspb.2004.2864
Categories¶
biology, phylogenetics