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Simulate DNA sequences for the node substitution model. In the node substitution model, substitutions accumulate additionally during a speciation event, providing a potential mechanistic explanation for substitution rate variation. This package provides tools to simulate such a process, simulate a reference process with only substitutions along the branches, and provides tools to infer phylogenies from alignments. More information can be found in Janzen (2021) <doi:10.1093/sysbio/syab085>.
| Version: | 1.2.8 |
| Depends: | Rcpp, ape |
| Imports: | phangorn, tibble, DDD, Rmpfr, pbapply, phylobase, geiger, beautier, beastier, tracerer, rappdirs, testit, stringr, lifecycle |
| LinkingTo: | Rcpp |
| Suggests: | testthat, TreeSim, dplyr, knitr, rmarkdown, ggplot2, magrittr, tidyr, nLTT, RPANDA |
| Published: | 2023-11-14 |
| Author: | Thijs Janzen |
| Maintainer: | Thijs Janzen <thijsjanzen at gmail.com> |
| BugReports: | https://github.com/thijsjanzen/nodeSub |
| License: | GPL-3 |
| URL: | https://github.com/thijsjanzen/nodeSub |
| NeedsCompilation: | yes |
| Materials: | README |
| CRAN checks: | nodeSub results |
| Reference manual: | nodeSub.pdf |
| Vignettes: |
substitution_models |
| Package source: | nodeSub_1.2.8.tar.gz |
| Windows binaries: | r-devel: nodeSub_1.2.8.zip, r-release: nodeSub_1.2.8.zip, r-oldrel: nodeSub_1.2.8.zip |
| macOS binaries: | r-release (arm64): nodeSub_1.2.8.tgz, r-oldrel (arm64): nodeSub_1.2.8.tgz, r-release (x86_64): nodeSub_1.2.8.tgz, r-oldrel (x86_64): nodeSub_1.2.8.tgz |
| Old sources: | nodeSub archive |
| Reverse suggests: | treestats |
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