The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
APE: Analyses of Phylogenetics and Evolution in R language
Abstract
Summary: Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. Availability: The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.
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In the citing paper
“many ancestral likelihood inference methods model the probability of phenotype change as a function of branch length (Pagel 1994; Pupko et al. 2000; Paradis et al. 2004).”
From RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution (2024) · cites this paper as Paradis et al. 2004
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“we implemented maximum likelihood ancestral trait reconstruction using a continuous time Markov model of evolution; a framework that has been commonly applied to categorical traits (Pagel 1994; Pupko et al. 2000; Paradis et al. 2004).”
From RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution (2024) · cites this paper as Paradis et al. 2004
In the citing paper
“Reconstruction certainty, among many factors, depends on inferred phylogeny branch lengths which are related to evolutionary rates.”
From RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution (2024) · cites this paper as Paradis et al. 2004
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Citations
Cites
Phylogenies and the Comparative Method
Felsenstein, J. (1985) · The American Naturalist · doi:10.1086/284325 · Cited by 9,793
A nonparametric approach to estimating divergence times in the absence of rate constancy.
Sanderson, M. J. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025731 · Cited by 1,156 · cited 2×
“…models (Nee et al. , 1994; Pybus & Harvey, 2000), population-genetic analysis (Nee et al. , 1995; Strimmer & Pybus, 2001), non-parametric smoothing of evolutionary rates (Sanderson, 1997), and estimation of groups of genes in phylogenetic trees using Klastorin’s method (Misawa & Tajima, 2000).”
Flagged first, then by citations
Research works printed but not linked: 4
- Harvey,P.H. and Pagel,M.D. (1991) The Comparative Method in Evolutionary Biology. Oxford University Press, Oxford.
- Nee,S., Holmes,E.C., Rambaut,A. and Harvey,P.H. (1995) Inferring population history from molecular phylogenies. Phil. Trans. R. Soc. Lond. B, 349, 25-31.
- Nee,S., May,R.M. and Harvey,P.H. (1994) The reconstructed evolu- tionary process. Phil. Trans. R. Soc. Lond. B, 344, 305-311.
- Pybus,O.G. and Harvey,P.H. (2000) Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Lond B, 267, 2267-2272.
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Metadata
- Authors
- Paradis, E., Claude, J., & Strimmer, K.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-01-22
- Volume
- 20
- Issue
- 2
- Pages
- 289-290
- ISSN
- 1367-4811
- 1367-4803
- Cited by
- 11,335
- References
- 2
- Language
- en
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