adephylo specifications

Information


Unique identifier OMICS_08682
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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Documentation


Maintainer


  • person_outline Stéphane Dray <>

adephylo article

adephylo citations

 (2)
2015
PMCID: 4607533

[…] 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 […]

2013
PMCID: 3703296

[…] using treeannotator v1.6.2 [78]. the initial 1000 trees were discarded as burn-in. abouheif proximities were computed from the phylogenetic trees using the function ‘proxtips’ in the package ‘adephylo’ in r [79]., pairwise genetic distances for the 12s and rhodopsin nucleotide sequences were computed using the software mega [66]. both transition and transversion nucleotide substitutions […]

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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