[Molecular-evolution] Re: re-drawing trees with overlapping labels

Don Gilbert via mol-evol%40net.bio.net (by gilbertd from bio.indiana.edu)
Thu Jun 3 10:42:34 EST 2010


Guy,

It may be possible for you to use PHYLIP's drawtree for this if you want,
by adding inner node labels to a newick format tree from your PhyML/MrBayes
output.  I do this occassionally, draw trees with Phylodendron web form,
which is based on Joe Felsenstein's drawtree.  I save the output as PDF,
then I use a PDF editor (adobe illustrator, others will work),
to clean up overlapping labels as needed.  

Here is an example newick tree with inner node labels (e.g. mosquito_, insect_)
that you can test at http://iubio.bio.indiana.edu/treeapp/treeprint-form.html

-- Don Gilbert

# Arthropod gene tree
(daphnia:0.35686,
((bombyx:0.32420,
(((culex:0.19487,aedes:0.17350):0.03977,anophel:0.19417
 )mosquito_0.10789:0.10789,
((drosmel:0.13957,drospse:0.17919):0.03863,drosmoj:0.20635
 )drosophila_0.15143:0.15143
)diptera_0.01822:0.01822

):0.01040,((aphid:0.37147,pedicul:0.24481):0.01177,(tribol:0.29044,
(apis:0.21818,nasonia:0.27637)hymenoptera_0.08571:0.08571
):0.00070
):0.00902
)insect_0.04882:0.04882,
ixodes:0.35973);

On 2010-06-03, Bottu Guy <gbottu from vub.ac.be> wrote:
> One of our users has a problem : his phylogenetic trees contain many
> taxons and the names tend to overlap. For trees made with the PHYLIP
> programs seqboot-dnapars-consense a method that works is to use
> drawtree, which has various algorithms to re-draw the branches and the
> labels in various orientations. But for trees made with PhyML or
> MrBayes, and that have included bootstrap values, there is a problem.
> The popular tree editor TreeView does not allow to re-orient the labels.
> Does someone know a way to do it (either using a performant tree editor
> or by procesing the pictorial representation of the tree in an image
> editor, preferable freeware) ?
>
>         Regards,
>         Guy Bottu,
>         Belgian EMBnet Node
>



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