I would like to color a phylogeny with criteria. i.e. highlight some specific sections of the tree (like attached). Can anyone recommend me a function or software to do it?
I appreciate your comments.
Try:
FigTree: http://tree.bio.ed.ac.uk/software/figtree/
EvolView: http://www.evolgenius.info/evolview/
Try:
FigTree: http://tree.bio.ed.ac.uk/software/figtree/
EvolView: http://www.evolgenius.info/evolview/
Hi,
you can rely on some web tools such as compphy (http://www.atgc-montpellier.fr/compphy/) or itol (http://itol.embl.de/upload.cgi ) or the R package APE (http://rstudio-pubs-static.s3.amazonaws.com/1876_df0bf890dd54461f98719b461d987c3d.html) or treedyn (http://www.treedyn.org/). In fact there is a lot of good tools for coloring phylogenetic trees rather easily either via a graphical interface or via small scripts ...
hope this help,
Vincent Ranwez
I also forgot to mention the ETE package for Python: http://etetoolkit.org/
Additional to FigTree, I also like Dendroscope (http://dendroscope.org/)
I think the best and probably easiest tool to use would be IToL (http://itol.embl.de). See more details under the 'upload and working with your own trees section' from http://itol.embl.de/help/help.shtml
In R you can use the plot function (with options edge.color="col" and tip.color="col") in the analyses of phylogenetics and evolution (APE) R package (https://cran.r-project.org/web/packages/ape/ape.pdf). The paper is available here http://bioinformatics.oxfordjournals.org/content/20/2/289.abstract
Hi Soraya,
Try GraPhlAn (https://bitbucket.org/nsegata/graphlan/wiki/Home) for producing high-quality circular representations of phylogenetic trees.
Yes, I agree, I use Figtree in order to colour my clades. It's very simple and easy.
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