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rtrees  

Deriving Phylogenies from Synthesis Trees
View on CRAN: Click here


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

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

Install by package version:
library("remotes")
install_version("rtrees", "2.0.2")



Attach the package and use:
library("rtrees")
Maintained by
Daijiang Li
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-06-11
Latest Update: 2026-06-11
Description:
Provides tools to derive species-level phylogenies from large synthesis mega-trees for a wide range of taxonomic groups, including plants, birds, mammals, amphibians, reptiles, fish, bees, butterflies, and sharks. When a queried species is absent from the mega-tree, it is grafted onto the tree using one of two placement strategies: attachment at the basal node of the most closely related genus or family ('at_basal_node'), or random attachment below that basal node with probability proportional to branch length ('random_below_basal'). See Li (2023) <doi:10.1111/ecog.06643> for details. Multiple species from a genus not represented in the mega-tree are placed as a polytomy to preserve clade coherence. The package interfaces with the 'megatrees' data package, which bundles or downloads on demand curated mega-trees. Users can also provide their own mega-trees.
How to cite:
Daijiang Li (2026). rtrees: Deriving Phylogenies from Synthesis Trees. R package version 2.0.2, https://cran.r-project.org/web/packages/rtrees. Accessed 22 Jun. 2026.
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