ArticleBMC research notes2017
treeman: an R package for efficient and intuitive manipulation of phylogenetic trees.
Article in BMC research notes, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed, 24 citations in OpenAlex.
- 'gitana' (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures.BMC bioinformatics · 2025Article
- Common Methods for Phylogenetic Tree Construction and Their Implementation in R.Bioengineering (Basel, Switzerland) · 2024Review
- Assessing global drivers of parasite diversity: host diversity and body mass boost avian haemosporidian diversity.Parasitology · 2024Article
- Host phylogeny and seasonality shapes avian haemosporidian prevalence in a Brazilian biodiverse and dry forest: the Caatinga.Parasitology · 2023Article
- Migratory behaviour does not alter cophylogenetic congruence between avian hosts and their haemosporidian parasites.Parasitology · 2022Article
- Historical, archaeological and linguistic evidence test the phylogenetic inference of Viking-Age plant use.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2021Article
- The Legacy of Recurrent Introgression during the Radiation of Hares.Systematic biology · 2021Article
- Within-individual phenotypic plasticity in flowers fosters pollination niche shift.Nature communications · 2020Article
- Article
- How the past impacts the future: modelling the performance of evolutionarily distinct mammals through time.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Sperm morphology and evidence for sperm competition among parrots.Journal of evolutionary biology · 2019Article
- phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R.Life (Basel, Switzerland) · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPhylogenetic trees are hierarchical structures used for representing the inter-relationships between biological entities. They are the most common tool for representing evolution and are essential to a range of fields across the life sciences. The manipulation of phylogenetic trees-in terms of adding or removing tips-is often performed by researchers not just for reasons of management but also for performing simulations in order to understand the processes of evolution. Despite this, the most common programming language among biologists, R, has few class structures well suited to these tasks.
resultsWe present an R package that contains a new class, called TreeMan, for representing the phylogenetic tree. This class has a list structure allowing phylogenetic trees to be manipulated more efficiently. Computational running times are reduced because of the ready ability to vectorise and parallelise methods. Development is also improved due to fewer lines of code being required for performing manipulation processes.
conclusionsWe present three use cases-pinning missing taxa to a supertree, simulating evolution with a tree-growth model and detecting significant phylogenetic turnover-that demonstrate the new package's speed and simplicity.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.