Article View: bionet.molbio.evolution
Article #368Re: re-drawing trees with overlapping labels
From: Don Gilbert
Date: Thu, 03 Jun 2010 15:42
Date: Thu, 03 Jun 2010 15:42
46 lines
4251 bytes
4251 bytes
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@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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