treespace statistics

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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

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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 in publications

 (10)
PMCID: 5865477
PMID: 29576986
DOI: 10.7717/peerj.4529

[…] 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 […]

PMCID: 5715027
PMID: 29051535
DOI: 10.1038/s41467-017-01223-x

[…] (supplementary fig. , rows 2 and 3)., 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 , […]

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

[…] (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 […]

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

[…] 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) […]

PMCID: 5598434
PMID: 28924504
DOI: 10.7717/peerj.3790

[…] was assessed using r package rwty (). for both analyses, all parameters have converged within the first fifty million generations. the tree topologies took much longer to converge, as judged with treespace plots. based on this information, the burn-in was set to 580 million generations for nucleotide trees and 150 million generations for amino acid trees. both posterior tree sets were used […]


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treespace institution(s)
Department of Mathematics, Imperial College London, London, UK; Oxford Big Data Institute, Oxford, UK

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