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.