CoalescentPhylo: Phylogenetics via Root Distances Method Under the Coalescent

Estimates phylogenetic trees from allele count data using the root distance method under the Coalescent Model. Given a matrix of allele counts across taxa and loci, the package estimates pairwise root distances under the Coalescent Model using maximum likelihood estimation. Then, it estimates a labeled phylogenetic tree from the estimated root distances. See Peng et al. (2021) <doi:10.1016/j.ympev.2021.107142>.

Version:	0.1.0
Depends:	R (≥ 3.5.0)
Imports:	ape, parallel, pbapply, phangorn, rootSolve
Published:	2026-05-27
DOI:	10.32614/CRAN.package.CoalescentPhylo
Author:	Arindam RoyChoudhury [aut, cre, cph], Ying Li [aut]
Maintainer:	Arindam RoyChoudhury <arr2014 at med.cornell.edu>
BugReports:	https://github.com/ArindamRoyChoudhury/CoalescentPhylo/issues
License:	AGPL-3
URL:	https://github.com/ArindamRoyChoudhury/CoalescentPhylo
NeedsCompilation:	no
Materials:	NEWS
CRAN checks:	CoalescentPhylo results

Documentation:

Reference manual:

CoalescentPhylo.html , CoalescentPhylo.pdf

Downloads:

Package source:	CoalescentPhylo_0.1.0.tar.gz
Windows binaries:	r-devel: CoalescentPhylo_0.1.0.zip, r-release: CoalescentPhylo_0.1.0.zip, r-oldrel: CoalescentPhylo_0.1.0.zip
macOS binaries:	r-release (arm64): CoalescentPhylo_0.1.0.tgz, r-oldrel (arm64): CoalescentPhylo_0.1.0.tgz, r-release (x86_64): CoalescentPhylo_0.1.0.tgz, r-oldrel (x86_64): CoalescentPhylo_0.1.0.tgz

Linking:

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