treespace statistics

info info

Citations per year

info

Tool usage distribution map

info info

Associated diseases

info

Popular tool citations

chevron_left Phylogenetic comparative analysis chevron_right
Want to access the full stats & trends on this tool?

Protocols

treespace specifications

Information


Unique identifier OMICS_26837
Name treespace
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License MIT License
Computer skills Advanced
Version 1.1.3
Stability Stable
Requirements
RColorBrewer, parallel, utils, testthat, Rcpp, ggplot2, rmarkdown, knitr, MASS, fields, reshape2, igraph, ade4, combinat, htmlwidgets, shiny, rgl, pander, ape, distory, adegenet, phangorn, phytools, compiler, R(≥3.4.0), shinyBS, adegraphics, adephylo, RLumShiny, scatterD3
Maintained Yes

Versioning


No version available

Documentation


Maintainer


Additional information


A Shiny app is also available : http://shiny.imperial-stats-experimental.co.uk/users/mlkendal/treespace

Information


Unique identifier OMICS_26837
Name treespace
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


Additional information


A Shiny app is also available : http://shiny.imperial-stats-experimental.co.uk/users/mlkendal/treespace

Publications for treespace

treespace citations

 (21)
library_books

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

2018
Wellcome Open Res
PMCID: 5930550
PMID: 29774245
DOI: 10.21956/wellcomeopenres.15526.r32391

[…] s/which_tree (GPLv2 license)Distances of real gene trees: https://gist.github.com/johnlees/da164a4260e13528e8315e266a46bf3f Inferred trees: https://dx.doi.org/10.6084/m9.figshare.5483464 Interactive treespace plots: https://dx.doi.org/10.6084/m9.figshare.5923300 Simulation parameters and results (including true alignments of all genes, assemblies and annotations from simulated reads): https://dx […]

library_books

TreeTime: Maximum likelihood phylodynamic analysis

2018
Virus Evol
PMCID: 5758920
PMID: 29340210
DOI: 10.1093/ve/vex042

[…] nes nextstrain and nextflu (). TreeTime tries to strike a useful compromise between inflexible but fast heuristics and computationally expensive Bayesian approaches that require extensive sampling of treespace. The overarching algorithmic strategy is iterative optimization of efficiently solvable subproblems to arrive at a consistent approximation of the global optimum. Although this strategy is a […]

library_books

The systematic position of the enigmatic thyreophoran dinosaur Paranthodon africanus, and the use of basal exemplifiers in phylogenetic analysis

2018
PeerJ
PMCID: 5865477
PMID: 29576986
DOI: 10.7717/peerj.4529

[…] use of ‘New Technology’ searches, rather than the ‘Traditional’ search option used in the original analysis. ‘Traditional’ searches are heuristic, and can get stuck on local parsimony optimums within treespace, whereas ‘New Technology’ searches employ algorithms (Ratchet, Sectorial, Drift and Tree Fusing) that allow more rigorous searches for improved tree scores and a reduced number of optimal tr […]

call_split

The biomechanical origin of extreme wing allometry in hummingbirds

2017
Nat Commun
PMCID: 5715027
PMID: 29051535
DOI: 10.1038/s41467-017-01223-x
call_split See protocol

[…] All analyses were performed with R 3.2.0 to organise data and interface with JAGS 4.2). We also used the R package dplyr for data manipulation; ape, nlme and treespace , , for phylogeny manipulation, visualisation of phylogenetic uncertainty, and comparison of our parameter estimates to those obtained by maximum likelihood; and rjags and R2jags , for int […]

library_books

Austromonticola, a new genus of broad nosed weevil (Coleoptera, Curculionidae, Entiminae) from montane areas of New Zealand

2017
Zookeys
PMCID: 5674147
PMID: 29118629
DOI: 10.3897/zookeys.707.12649

[…] hangorn (version 2.0.4) (), using Fitch parsimony with a random starting tree and subtree pruning and regrafting (SPR) rearrangements. The ratchet was run 100 times to ensure thorough sampling of the treespace. Bootstrap and jackknife (delete-half method, ) support values were calculated using Phangorn with 100 replicates each. Due to A. planulatus, A. caelibatus and A. postinventus not having sui […]

library_books

Membrane Trafficking Modulation during Entamoeba Encystation

2017
Sci Rep
PMCID: 5634486
PMID: 28993644
DOI: 10.1038/s41598-017-12875-6

[…] mum-Likelihood analyses. Phylobayes was run until the largest discrepancy observed across all bipartitions was less than 0.1 and at least 100 sampling points were achieved, MrBAYES was used to search treespace for a minimum of one million MCMC generations, sampling every 1000 generations, until the average standard deviation of the split frequencies of two independent runs (with two chains each) w […]


Want to access the full list of citations?
treespace institution(s)
Department of Mathematics, Imperial College London, London, UK; Oxford Big Data Institute, Oxford, UK

treespace reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review treespace