GEIGER
GEIGER is an R tool to analyze, simulate, and estimate parameters for evolutionary radiations. The GEIGER algorithm includes functions for statistical hypothesis testing and analyzing the statistical power. Among others, the GEIGER package includes the following published methods: Time-scaling large phylogenies with 'congruification,' identifying shifts in the rate of diversification, identifying shifts in the rate of diversification, using fossil information to improve macroevolutionary inference, fitting discrete models of evolution, fit continuous trait models to unresolved data using ABC, identify shifts in the rate of continuous trait evolution, fit continuous models of evolution, and fit discrete models of evolution.
Topic
Phylogenetics;Statistics and probability;Evolutionary biology
Detail
Operation: Phylogenetic tree generation
Software interface: Library
Language: R
License: GNU General Public License v2 | v3
Cost: Free
Version name: 2.0.10
Credit: University of British Columbia Biodiversity Research Centre, NSF IGERT Fellowship.
Input: -
Output: -
Contact: Luke Harmon lukeh@uidaho.edu
Collection: -
Maturity: -
Publications
- GEIGER: investigating evolutionary radiations.
- Harmon LJ, Weir JT, Brock CD, Glor RE, Challenger W. GEIGER: investigating evolutionary radiations. Bioinformatics. 2008 Jan 1;24(1):129-31. doi: 10.1093/bioinformatics/btm538. Epub 2007 Nov 15. PMID: 18006550.
- https://doi.org/10.1093/bioinformatics/btm538
- PMID: 18006550
- PMC: -
- geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees.
- Pennell MW, Eastman JM, Slater GJ, Brown JW, Uyeda JC, FitzJohn RG, Alfaro ME, Harmon LJ. geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. Bioinformatics. 2014 Aug 1;30(15):2216-8. doi: 10.1093/bioinformatics/btu181. Epub 2014 Apr 10. PMID: 24728855.
- https://doi.org/10.1093/bioinformatics/btu181
- PMID: 24728855
- PMC: -
Download and documentation
Source: https://cran.r-project.org/src/contrib/geiger_2.0.10.tar.gz
Documentation: https://cran.r-project.org/web/packages/geiger/geiger.pdf
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