adephylo pipeline

adephylo specifications


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 1.1-6
Stability Stable
Requirements methods, ade
Maintained Yes


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  • person_outline Stéphane Dray <>

Publication for adephylo

adephylo IN pipelines

PMCID: 5324663
PMID: 27037681
DOI: 10.1111/mec.13636

[…] of cephalodia or volumes of cephalodia per area. we created phylogenetic and morphometric character coplots (i.e. combinations of trees and bar plots) using custom r scripts using the packages ape, adephylo (jombart et al. 2010) and phylobase (bolker et al. 2010; hackathon et al. 2011). plotted characters include the relative mean thallus thickness, mean hymenial volume and hymenial volume per […]

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 fig. 3) using the “table.phylo4d” function of the adephylo package (jombart and dray 2010). the phylogenetic tree of sela proteins was obtained using the maximum-likelihood method implemented in the raxml program ver. 7.7.8 (stamatakis 2006) using […]

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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