scistreer: Maximum-Likelihood Perfect Phylogeny Inference at Scale

Fast maximum-likelihood phylogeny inference from noisy single-cell data using the 'ScisTree' algorithm by Yufeng Wu (2019) <doi:10.1093/bioinformatics/btz676>. 'scistreer' provides an 'R' interface and improves speed via 'Rcpp' and 'RcppParallel', making the method applicable to massive single-cell datasets (>10,000 cells).

Version:	1.2.1
Depends:	R (≥ 4.1.0)
Imports:	ape, dplyr, ggplot2, ggtree, igraph, parallelDist, patchwork, phangorn, Rcpp, reshape2, RcppParallel, RhpcBLASctl, stringr, tidygraph
LinkingTo:	Rcpp, RcppArmadillo, RcppParallel
Suggests:	testthat (≥ 3.0.0)
Published:	2026-02-05
DOI:	10.32614/CRAN.package.scistreer
Author:	Teng Gao [cre, aut], Evan Biederstedt [aut], Peter Kharchenko [aut], Yufeng Wu [aut]
Maintainer:	Teng Gao <tgaoteng at gmail.com>
License:	GPL-3
URL:	https://github.com/kharchenkolab/scistreer, https://kharchenkolab.github.io/scistreer/
NeedsCompilation:	yes
SystemRequirements:	GNU make
Materials:	README
CRAN checks:	scistreer results

Documentation:

Reference manual:

scistreer.html , scistreer.pdf

Downloads:

Package source:	scistreer_1.2.1.tar.gz
Windows binaries:	r-devel: scistreer_1.2.1.zip, r-release: scistreer_1.2.1.zip, r-oldrel: scistreer_1.2.1.zip
macOS binaries:	r-release (arm64): scistreer_1.2.1.tgz, r-oldrel (arm64): scistreer_1.2.1.tgz, r-release (x86_64): scistreer_1.2.1.tgz, r-oldrel (x86_64): scistreer_1.2.1.tgz
Old sources:	scistreer archive

Reverse dependencies:

Reverse imports:

numbat

Linking:

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