adephylo protocols

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adephylo specifications

Information


Unique identifier OMICS_08682
Name adephylo
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 2.0
Computer skills Advanced
Version 1.1-11
Stability Stable
Requirements
methods, ape, ade4(≥1.7-10), phylobase, adegenet
Maintained Yes

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Maintainer


  • person_outline Stéphane Dray <>

Publication for adephylo

adephylo in pipelines

 (4)
2016
PMCID: 4907049
PMID: 27296936
DOI: 10.1186/s12864-016-2738-7

[…] to the free kegg database from 2011 and compared across metabolic pathways []. a grid that correlates highlighted kegg comparisons with the phylogenomic tree described above was generated using the adephylo package in r []., anabaena sp. wa102 [genbank:cp011456-7], anabaena sp. al93 [genbank:ljou00000000], dolichospermum sp. awqc131c, dolichospermum sp. awqc310f, anabaena variabilis atcc 29413 […]

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

[…] green algae published to date., for each trait, we chose to calculate three commonly used metrics of phylogenetic signal: blomberg's k, pagel's λ, and moran's i using the picante, geiger and adephylo packages in r respectively [–]. p-values for the significance of k and i were based on 999 randomizations each, whereas the significance test for λ was based on a likelihood ratio test. k […]

2015
PMCID: 4607533
PMID: 26342139
DOI: 10.1093/gbe/evv177

[…] and the resulting tree was rendered ultrametric with the “chronos” function. traits of gene presence/absence were plotted alongside the tips (see ) using the “table.phylo4d” function of the adephylo package (). the phylogenetic tree of sela proteins was obtained using the maximum-likelihood method implemented in the raxml program ver. 7.7.8 () using the protcatgtr amino acid […]

2012
PMCID: 3364262
PMID: 22666324
DOI: 10.1371/journal.pone.0036664

[…] accessed 13 april 2012), picante , phytools (cran - package phytools. available: http://cran.r-project.org/package=phytools. accessed 13 april 2012) and adephylo packages., a composite phylogenetic tree () for use with pcms was constructed in mesquite 2.75 (mesquite. available: http://mesquiteproject.org. accessed 13 april 2012). the topology […]


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adephylo in publications

 (33)
PMCID: 5809455
PMID: 29434223
DOI: 10.1038/s41598-018-21188-1

[…] ads parameters were analyzed together in phytools package after scaling and centralizing the data, while the positive and negative scores for each trait were displayed in the aegla’s phylogeny using adephylo. for those parameters correlated with the two main eigenvectors and with explained variance higher than 60%, we have tested for each one hypotheses of co-variation between ads […]

PMCID: 5800076
PMID: 29402215
DOI: 10.1186/s12864-017-4417-8

[…] the opsin ω-trees (i.e. a ω-tree linearization), were calculated and standardized to identify ω-lineage outlier tendencies. the ω-lineage was calculated using the distroot(tree,tips) function of the adephylo package of the r statistical software [, ]. statistically significant ω-lineage variations in specific branches were tested via lrt using the one-ratio vs. the two-ratio model comparison: […]

PMCID: 5740905
PMID: 29268709
DOI: 10.1186/s12870-017-1199-8

[…] were trimmed to keep only these 14 tips using the function drop.tip() in the r package ape [] and the patristic root-to-tip distances were computed using the distroot() function in the r package adephylo []., we first implied a simple linear regression method using the lm() function in r [] on log-transformed flowering cycles and patristic distances calculated from unpartitioned ml tree […]

PMCID: 5743486
PMID: 29299283
DOI: 10.1002/ece3.3564

[…] on the three metrics blomberg’ k (blomberg, garland, & ives, ), pagel's λ (pagel, ), and abouheif/moran's i (abouheif, ) (table ), and calculated in the r‐packages “phytools” (revell, ) and “adephylo” (jombart, balloux, & dray, ), for the subset of 121 species (of the 143 angiosperm species occurring in the 27 plots) for which data on all six traits were available from kröber et al. […]

PMCID: 5723631
PMID: 29238527
DOI: 10.1002/ece3.3420

[…] phylogenetic signal (autocorrelation) was tested on each synthetic variable by abouheif's test (abouheif, ; pavoine, ollier, pontier, & chessel, ). these methods were performed using the adephylo package of r (r core team, ). the reconstruction of ancestral states of the four syndromes suggested that strategy b should be subdivided in two groups. thereby the first three components […]


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adephylo institution(s)
Department of Infectious Disease Epidemiology, Imperial College - Faculty of Medicine, MRC Centre for Outbreak Analysis and Modelling, St Marys Campus, Norfolk Place, London, UK; Université de Lyon, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
adephylo funding source(s)
BBSRC and MRC; ANR Diversitalp (ANR 07 BDIV 014)

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