‘ConsTree’ is an R package providing a comprehensive, efficient suite of methods for summarizing a collection of phylogenetic trees — for example a bootstrap or Bayesian posterior sample — as a single consensus tree.
Consensus methods
Split-selection methods
These methods take a list of trees (or a multiPhylo) that share the same leaves, and return a single phylo object. Methods differ in which groupings (splits or clusters) the consensus tree retains:
| Function | Objective |
|---|---|
Strict() |
Retains groupings that occur in every tree |
Majority() / MajorityRule()
|
Retains groupings that occur in most trees (tunable via p) |
Loose() |
Retains groupings that no tree contradicts (semi-strict / combinable-component) |
MajorityPlus() |
Retains groupings that more trees display than contradict |
Frequency() |
Retains groupings that are more frequent than every conflicting grouping (frequency-difference) |
Greedy() |
Adds groupings greedily, most frequent first, when compatible with those already kept (extended majority-rule) |
Adams() |
Constructed from the finest root-level partition shared by every tree (may introduce novel groupings; rooted) |
Local() |
Built from rooted triplets shared by every tree (minimum rooted/induced local consensus; ≤ 20 leaves) |
RStar() |
Includes each rooted triplet grouping that wins a plurality against each alternative separately |
Distance and branch-length summaries
These methods summarize trees through a distance or tree-space criterion:
| Function | Objective |
|---|---|
Average() |
The tree best fitting the mean path-length (patristic) distances of the inputs |
Quartet() |
An approximate median minimizing the total quartet distance to the inputs; often more resolved than majority-rule |
Transfer() |
A greedy consensus minimizing total transfer distance to the inputs; often more resolved than majority-rule |
BHVMean() |
the Fréchet mean tree in Billera–Holmes–Vogtmann treespace, with branch lengths; BHVDistance(), BHVPairwiseDistances() and BHVVariance() provide the supporting geodesic distances and dispersion |
Usage
library("ConsTree")
trees <- ape::as.phylo(1:100, 8) # 100 eight-leaf trees
Strict(trees) # most conservative
Majority(trees) # the familiar 50% majority-rule tree
Loose(trees) # everything not actively contradicted
Frequency(trees) # frequency-difference: often more resolved than majority
Greedy(trees) # most resolved of the split-based summaries
Transfer(trees) # minimizes transfer distance; often more resolved than majority-ruleInstallation
Install from CRAN (anticipated Oct 2026) with:
install.packages("ConsTree")Install the development version from GitHub:
if (!require("pak")) install.packages("pak")
pak::pkg_install("ms609/ConsTree")Relationship to other packages
‘ConsTree’ builds on TreeTools (the fast engine for strict and majority-rule consensus calculation) and ‘TreeDist’ (tree distances and information-theoretic consensus).
‘TreeDist’’s median.multiPhylo offers a complementary summary: the tree within a sample that has the lowest median clustering information distance to the others.
The quartet machinery underlying Quartet() builds on the ‘Quartet’ package, which counts the resolved- and shared-quartet statistics between trees; and the BHV summaries relate to ‘distory’, which computes geodesic distances in the same treespace.
‘Rogue’ identifies unstable wildcard leaves whose removal can improve the resolution and support of a consensus tree; dropping rogue taxa before summarizing with ‘ConsTree’ often leads a reduced consensus tree with increased resolution.
Citation and attribution
The manual page for each function details the literature that underpins each method; please cite this literature alongside this package (type citation("ConsTree")).
Please note that this project is released with a Contributor Code of Conduct. By contributing, you agree to abide by its terms.
