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phyclust  

Phylogenetic Clustering (Phyloclustering)
View on CRAN: Click here


Download and install phyclust package within the R console
Install from CRAN:
install.packages("phyclust")

Install from Github:
library("remotes")
install_github("cran/phyclust")

Install by package version:
library("remotes")
install_version("phyclust", "0.1-34")



Attach the package and use:
library("phyclust")
Maintained by
Wei-Chen Chen
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2010-01-29
Latest Update: 2023-09-06
Description:
Phylogenetic clustering (phyloclustering) is an evolutionary Continuous Time Markov Chain model-based approach to identify population structure from molecular data without assuming linkage equilibrium. The package phyclust (Chen 2011) provides a convenient implementation of phyloclustering for DNA and SNP data, capable of clustering individuals into subpopulations and identifying molecular sequences representative of those subpopulations. It is designed in C for performance, interfaced with R for visualization, and incorporates other popular open source programs including ms (Hudson 2002) , seq-gen (Rambaut and Grassly 1997) , Hap-Clustering (Tzeng 2005) and PAML baseml (Yang 1997, 2007) , , for simulating data, additional analyses, and searching the best tree. See the phyclust website for more information, documentations and examples.
How to cite:
Wei-Chen Chen (2010). phyclust: Phylogenetic Clustering (Phyloclustering). R package version 0.1-34, https://cran.r-project.org/web/packages/phyclust. Accessed 22 Dec. 2024.
Previous versions and publish date:
0.1-1 (2010-01-29 08:53), 0.1-2 (2010-02-18 17:53), 0.1-3 (2010-02-19 15:44), 0.1-4 (2010-02-21 19:43), 0.1-5 (2010-02-22 09:05), 0.1-6 (2010-04-10 08:33), 0.1-7 (2010-04-27 21:10), 0.1-8 (2010-09-19 20:30), 0.1-9 (2011-10-26 20:00), 0.1-10 (2011-11-06 09:39), 0.1-11 (2012-03-11 07:35), 0.1-12 (2012-06-06 08:05), 0.1-13 (2012-12-26 09:25), 0.1-14 (2013-01-08 19:18), 0.1-15 (2013-12-14 20:31), 0.1-16 (2015-12-04 08:40), 0.1-17 (2016-07-15 10:14), 0.1-18 (2016-12-11 12:26), 0.1-19 (2017-04-29 23:20), 0.1-20 (2017-08-26 15:27), 0.1-21 (2017-11-18 19:58), 0.1-22 (2017-12-02 20:22), 0.1-23 (2019-03-08 14:50), 0.1-24 (2019-03-27 11:00), 0.1-25 (2019-08-25 11:20), 0.1-26 (2019-09-27 06:30), 0.1-27 (2019-11-29 13:00), 0.1-28 (2019-12-08 11:30), 0.1-29 (2020-05-11 19:00), 0.1-30 (2021-02-10 15:00), 0.1-32 (2022-10-25 08:22), 0.1-33 (2023-01-22 22:40)
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