Difference between revisions of "Sate"
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 21:24, 6 December 2019
Description
SATé is a software package for inferring a sequence alignment and phylogenetic tree. The iterative algorithm involves repeated alignment and tree searching operations. The original data set is divided into smaller subproblems by a tree-based decomposition. These subproblems are aligned and further merged for phylogenetic tree inference.
Environment Modules
Run module spider sate to find out what environment modules are available for this application.
System Variables
- HPC_SATE_DIR - installation directory
- HPC_SATE_BIN - executable directory
Citation
If you use the software in a publication, please cite the software, the papers describing the method, and the appropriate citation for the external tools. Algorithm citations
- Liu, K., S. Raghavan, S. Nelesen, C. R. Linder, T. Warnow, 2009. "Rapid and accurate large scale coestimation of sequence alignments and phylogenetic trees." Science, 324(5934), pp. 1561-1564, 19 June 2009, doi: 10.1126/science.1171243
- Liu, K., T.J. Warnow, M.T. Holder, S. Nelesen, J. Yu, A. Stamatakis, and C.R. Linder. "SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees." Systematic Biology. 61(1):90-106
Citations for the SATé software itself and its dependencies
- Jiaye Yu, and Mark T. Holder "SATé version VERSION_NUMBER_HERE" from http://phylo.bio.ku.edu/software/sate/sate.html DATE DOWNLOADED." (for version 1.2 or earlier)
- Jiaye Yu, Mark T. Holder, Jeet Sukumaran, and Siavash Mirarab "SATé version VERSION_NUMBER_HERE" from http://phylo.bio.ku.edu/software/sate/sate.html DATE DOWNLOADED." (for version 1.2.1 to 2.1.0)
- Jiaye Yu, Mark T. Holder, Jeet Sukumaran, Siavash Mirarab, and Jamie Oaks "SATé version VERSION_NUMBER_HERE" from http://phylo.bio.ku.edu/software/sate/sate.html DATE DOWNLOADED." (for version 2.2.0 or later)
- Sukumaran, J. and Mark T. Holder. 2010. "DendroPy: A Python library for phylogenetic computing". Bioinformatics 26: 1569-1571. (for all SATé versions from this website)