software-link.R

pacman::p_load(yulab.utils)

# pkg name in bold
options("yulab.utils_pkgfmt" = '**%s**') 

pkg_archaeopteryx <- mypkg("Archaeopteryx", "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx")
pkg_astral <- mypkg("ASTRAL", "https://github.com/smirarab/ASTRAL")
pkg_atv <- mypkg("ATV", "http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=atv")
pkg_baseml <- mypkg("BASEML", "http://abacus.gene.ucl.ac.uk/software/paml.html")
pkg_beast <- mypkg("BEAST", "http://beast2.org/")
pkg_codeml <- mypkg("CODEML", "http://abacus.gene.ucl.ac.uk/software/paml.html")
pkg_devout <- mypkg("devout", "https://github.com/coolbutuseless/devout")
pkg_epa <- mypkg("EPA", "http://sco.h-its.org/exelixis/web/software/epa/index.html")
pkg_evolview <- mypkg("EvolView", "https://www.evolgenius.info/evolview/")
pkg_figtree <- mypkg("FigTree", "http://beast.community/figtree")
pkg_hyphy <- mypkg("HyPhy", "https://veg.github.io/hyphy-site/")
pkg_itol <- mypkg("iTOL", "https://itol.embl.de/")
pkg_mega <- mypkg("MEGA", "https://www.megasoftware.net/")
pkg_mothur <- mypkg("mothur", "http://mothur.org/")
pkg_mrbayes <- mypkg("MrBayes", "http://nbisweden.github.io/MrBayes/")
pkg_paml <- mypkg("PAML", "http://abacus.gene.ucl.ac.uk/software/paml.html")
pkg_paup <- mypkg("PAUP\\*", "https://paup.phylosolutions.com/")
pkg_phyldog <- mypkg("PHYLDOG", "http://pbil.univ-lyon1.fr/software/phyldog/") 
pkg_phylip <- mypkg("PHYLIP", "https://evolution.genetics.washington.edu/phylip.html")
pkg_phyloch <- mypkg("PHYLOCH", "http://www.christophheibl.de/Rpackages.html")
pkg_phyml <- mypkg("PhyML", "http://www.atgc-montpellier.fr/phyml/")
pkg_pplacer <- mypkg("PPLACER", "http://matsen.fhcrc.org/pplacer/")
pkg_pyrotagger <- mypkg("PyroTagger", "http://pyrotagger.jgi-psf.org/")
pkg_qiime <- mypkg("QIIME", "http://qiime.org/")
pkg_r8s <- mypkg("r8s", "http://loco.biosci.arizona.edu/r8s/")
pkg_raxml <- mypkg("RAxML", "http://evomics.org/learning/phylogenetics/raxml/")
pkg_revbayes <- mypkg("RevBayes", "http://revbayes.github.io/intro.html")
pkg_treedataverse <- mypkg("treedataverse", "https://github.com/YuLab-SMU/treedataverse")
pkg_treedyn <- mypkg("TreeDyn", "http://www.treedyn.org/")
pkg_treeview <- mypkg("TreeView", "http://en.bio-soft.net/tree/TreeView.html")