GEIGER protocols

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GEIGER specifications

Information


Unique identifier OMICS_15703
Name GEIGER
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.6
Stability Stable
Requirements
methods, MASS, mvtnorm, digest, coda, colorspace, R(≥2.15.0), deSolve(≥1.7), subplex, ape(≥3.0-6), Rcpp(≥ 0.9.0), ncbit
Source code URL https://cran.r-project.org/src/contrib/geiger_2.0.6.tar.gz
Maintained Yes

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Maintainer


  • person_outline Matt Pennell <>

Publication for GEIGER

GEIGER in pipelines

 (2)
2018
PMCID: 5916309
PMID: 29721264
DOI: 10.1002/ece3.3925

[…] (2) regions, and (3) adaptive peaks estimated by surface, for each of the 100 trees sampled from the posterior distribution, using phytools (revell, ). models were implemented using the r packages geiger (harmon, weir, brock, glor, & challenger, ) and ouwie (beaulieu & o'meara, ) and compared by means of the sample size‐corrected akaike's information criterion (aicc)., we used mantel […]

2015
PMCID: 4562640
PMID: 26348482
DOI: 10.1371/journal.pone.0137085

[…] not display a significant signal, we asked whether alternative models provided a better explanation of trait variation. for each trait, we tested nine models of continuous trait evolution using the geiger package in r []., five of the nine potential models of evolution in the geiger package were retained for further analyses, either because they were the best fit model for one or more traits, […]


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GEIGER in publications

 (99)
PMCID: 5874073
PMID: 29590198
DOI: 10.1371/journal.pone.0195112

[…] were significantly more abundant in spring from both comparisons was then selected as those which had a preference for spring. significance of deseq results was determined by calculating pagel’s λ (geiger package []). deseq results were visualized alongside the verrucomicrobia tree using interactive tree of life [] and tree bootstrap values were calculated using the phangorn package []., […]

PMCID: 5888179
PMID: 29635329
DOI: 10.1093/gbe/evy063

[…] and intron content (group i and group ii introns) were separately mapped onto the ml tree. the following r packages were used: contmap function of phytools () for genome size analysis and ape (), geiger (), and phytools () for intron content. visualization was done using treegradients () or phytools., to assess putative origins and evolutionary histories of freestanding orfs (> 300 bp) […]

PMCID: 5853117
PMID: 29540154
DOI: 10.1186/s12862-018-1146-9

[…] older and younger splits using an r script., as an alternative approach to testing for temporal variation in the rate of character change (e.g. host shifts), we used the fitdiscrete function in the geiger r package [] to fit an equal rates likelihood model to the simplified host plant character matrix and phylogeny, then compared the resulting aikake information criterion (aic) score […]

PMCID: 5838057
PMID: 29531682
DOI: 10.1002/ece3.3880

[…] strimmer, ), and pagel's λ (freckleton, harvey, & pagel, ; pagel, ) was estimated for all biotic velocities, life history traits, and climatic tolerances using the fitcontinuous function in the geiger package (harmon, weir, brock, glor, & challenger, ); this process was repeated 100 times and the mean λ values recorded for each trait. note that resolving polytomies in this way […]

PMCID: 5792951
PMID: 29410874
DOI: 10.1098/rsos.171816

[…] on the two first pc axes (uncorrected for allometry) describing the main morphological variation, and using a relaxed brownian motion (bm) model with the function rjmcmc.bm as implemented in the geiger r package []. this flexible model allows the identification of rate changes (shifts) in trait evolution across lineages using a bayesian method based on reversible jump markov chain monte […]


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GEIGER funding source(s)
This work was supported by the University of British Columbia Biodiversity Research Centre and an NSF IGERT Fellowship (NSF BCS- 0549425).

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