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TESS: an R package for efficiently simulating phylogenetic trees and performing Bayesian inference of lineage diversification rates
- Source :
- Bioinformatics. 32:789-791
- Publication Year :
- 2015
- Publisher :
- Oxford University Press (OUP), 2015.
-
Abstract
- Summary: Many fundamental questions in evolutionary biology entail estimating rates of lineage diversification (speciation–extinction) that are modeled using birth–death branching processes. We leverage recent advances in branching-process theory to develop a flexible Bayesian framework for specifying diversification models—where rates are constant, vary continuously, or change episodically through time—and implement numerical methods to estimate parameters of these models from molecular phylogenies, even when species sampling is incomplete. We enable both statistical inference and efficient simulation under these models. We also provide robust methods for comparing the relative and absolute fit of competing branching-process models to a given tree, thereby providing rigorous tests of biological hypotheses regarding patterns and processes of lineage diversification. Availability and implementation: The source code for TESS is freely available at http://cran.r-project.org/web/packages/TESS/. Contact: Sebastian.Hoehna@gmail.com
- Subjects :
- 0106 biological sciences
0301 basic medicine
Statistics and Probability
Source code
Computer science
media_common.quotation_subject
Bayesian inference
computer.software_genre
010603 evolutionary biology
01 natural sciences
Biochemistry
03 medical and health sciences
Bayes' theorem
Diversification rates
Phylogenetics
Leverage (statistics)
Computer Simulation
Molecular Biology
Phylogeny
media_common
Phylogenetic tree
Bayes Theorem
Biological Evolution
Computer Science Applications
Computational Mathematics
R package
030104 developmental biology
Computational Theory and Mathematics
Programming Languages
Data mining
computer
Subjects
Details
- ISSN :
- 13674811 and 13674803
- Volume :
- 32
- Database :
- OpenAIRE
- Journal :
- Bioinformatics
- Accession number :
- edsair.doi.dedup.....0a228f63de4cb04f79928a22f602b812