Question: Software that allows tip label editing for phylogenetic trees?
0
gravatar for confusedious
3.5 years ago by
confusedious400
Australia
confusedious400 wrote:

I am currently trying to prepare some phylogenetic trees for publication and I am having some significant issues editing them.

The various phylogenetics packages and scripts I use render the tip labels in a number of different ways, none of which are attractive for publication. Geneious is my primary tree viewer, but it does not allow the editing of tip labels as far as I can see (one would have to re-name the sequences and re-create the tree - most of my tree building software is not in Geneioius and would lead to a circular problem).

The easiest solution I have found is to export a tree as a Newick file and then edit it manually, but this is horribly time consuming and also, I have discovered, causes me to loose bootstrap values for nodes.

Could anyone recommend a good tree editor in which I can edit tip labels? It would be great if the software could create publication quality figures as well.

Thank you for your time.

geneious phylogenetics • 2.8k views
ADD COMMENTlink modified 3.5 years ago by Abhiman130 • written 3.5 years ago by confusedious400

I usually do all the editing before plotting using ETE. If you don't mind to do some python scripting, load your newick as a python object, search for nodes, modify tip names, distances... and the export back as newick or plot directly using ETE. It shouldn't take more than a few lines. You have examples here 

ADD REPLYlink written 3.4 years ago by jhc2.7k
2
gravatar for Abhiman
3.5 years ago by
Abhiman130
Hyderabad, INDIA
Abhiman130 wrote:

I use treedyn (http://www.treedyn.org/) for this purpose. Sometimes even this does not solve the problem, I export the tree as vector image (SVG) or PDF and edit it in Inkscape (https://inkscape.org/). There are more suggestions in a related post on this topic A: What Phylogeny Viewing Software Do You Use?

ADD COMMENTlink written 3.5 years ago by Abhiman130
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