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Protocols

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 citations

 (45)
library_books

Phylogenetic and environmental components of inter specific variability in the antioxidant defense system in freshwater anomurans Aegla (Crustacea, Decapoda)

2018
Sci Rep
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 and environment […]

library_books

Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments

2018
BMC Genomics
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: the […]

library_books

Negative correlation between rates of molecular evolution and flowering cycles in temperate woody bamboos revealed by plastid phylogenomics

2017
BMC Plant Biol
PMCID: 5740905
PMID: 29268709
DOI: 10.1186/s12870-017-1199-8

[…] rees 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 based o […]

call_split

Phylogenetic turnover during subtropical forest succession across environmental and phylogenetic scales

2017
Ecol Evol
PMCID: 5743486
PMID: 29299283
DOI: 10.1002/ece3.3564
call_split See protocol

[…] re based 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. (), B […]

call_split

Ancestrality and evolution of trait syndromes in finches (Fringillidae)

2017
Ecol Evol
PMCID: 5723631
PMID: 29238527
DOI: 10.1002/ece3.3420
call_split See protocol

[…] r syndromes. 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 of […]

library_books

Estimating Herd Immunity to Amphibian Chytridiomycosis in Madagascar Based on the Defensive Function of Amphibian Skin Bacteria

2017
Front Microbiol
PMCID: 5604057
PMID: 28959244
DOI: 10.3389/fmicb.2017.01751

[…] s were compared to distances derived from mean inhibition scores of each isolate. Using the inferred phylogenetic tree, patristic distances between bacterial isolates were calculated with the ape and adephylo packages in R (Paradis et al., ; Jombart et al., ; R Core Team, ). Euclidean distances between mean inhibition scores were calculated in QIIME with the distance_matrix_from_mapping.py script. […]


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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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