Difference between revisions of "Clann"
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
|||
| Line 27: | Line 27: | ||
results is left entirely to the user. | results is left entirely to the user. | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | < | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| Line 85: | Line 75: | ||
<!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | <!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
| − | |||
| − | |||
Revision as of 13:56, 13 June 2022
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.
System 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:
Clann has been published in Bioinformatics in 2005 under the following title:
Creevey C.J. and McInerney J.O. 2005 Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 21(3): 390-2.
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. and McInerney J.O. 2004 Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proceedings of the Royal Society London, B series: Biological Sciences 271(1557): 2551-8.
Either or both of these publications should be cited if you use Clann in published work.