It seems as if I could productively conclude the theme of how to root phylogenetic trees by providing an overview of the tree viewers I have some experience with.
When you do a phylogenetic analysis in programs such as PAUP, TNT, RAxML, MrBayes or BEAST, you do get a phylogenetic tree, but it is not a graphic to look at. Instead, the standard format for phylogenetic trees is that of a text file in the Newick format, e.g. "(speciesA:4,(speciesB:6,(speciesC:2,speciesD:3)95:2)76:1)". The brackets show how the terminals of the tree are grouped, the numbers after the colons are branch lengths, and the other numbers following directly behind brackets are clade support values. All the information is there, but that is not a very clear way of displaying a tree, especially if it has dozens or hundreds of terminals.
The programs discussed below are used to display phylogenetic trees and to transform them into vector graphic files that can be used for the preparation of scientific publications.
The screen shots below show the same tree displayed in each program as a phylogram with clade support values.
Tree display: Radial phylogram; slanted cladogram; rectangular cladogram; rectangular phylogram. Ladderise left or right.
Branch labels: Simple branch labels (bootstraps or suchlike) but not complex ones from BEAST or newer MrBayes versions. They are always placed to the right of the branch instead of above
, which is rather unusual and rarely seen in scientific publications.
Rooting: Outgroup rooting.
Other formatting: Font size, type and effects can be changed but affect all terminals equally. Otherwise options are the most limited of all three programs.
Graphic export: Can export trees as EMF or WMF graphics, which is good for most vector graphics software but does not seem to work for the open source package Inkscape, or at least not for me.
Portability: Works well on Windows but is known to crash on Ubuntu, which is also my experience. There is also a Mac version.
Other comments: In my experience there are sometimes issues with the exported graphics, especially that the text is one line higher than it should be. This is no big problem for cladograms but very tedious to correct when working with phylograms.
Verdict: Easy to use and reliable on Windows but very limited in its functionality.
Tree display: Equal branch lengths, cladogram or proportional in any combination with rectangular, radial or circular tree layouts. For the rectangular display, it allows anything from slanted branches to right angles and even gentle arches.
Ladderise left or right ('branch order increasing or decreasing').
Branch labels: Can produce branch or node labels, with the former above the branches. Understands complex tree annotations from BEAST or newer MrBayes versions, with selection through a simple drop-down menu.
Rooting: Outgroup or midpoint rooting.
Other formatting: Overwhelming number of options for annotation, colouring, branch width, etc. This program really allows you to progress to publication readiness, but it can be hard to figure out how to do things, so I prefer to use graphics software at that step.
Graphic export: Can export trees as PDF, EPS, SVG, EMF and a variety of bitmap formats.
Portability: Very portable (Java).
Other comments: Strangely, branches and their half of the vertical line at the base of the clade are united into one L-shaped element in the exported graphic, which makes for some odd looking figures when branch width is increased to indicate high support values. In my experience there are often issues with each letter in terminal names exported as a separate element, making it hard to edit them later. Does not remember in what folder I last loaded or exported something, so that I have to navigate through the file system every time (grrr).
Verdict: I feel it is somewhat clunky and has several issues (see previous paragraph), but it is the most powerful of the three and without alternative for the heavily annotated Bayesian summary trees of BEAST and MrBayes.
Tree display: Rectangular phylogram; rectangular cladogram; slanted cladogram; circular phylogram; circular cladogram; inner circular cladogram (this one is really weird!); radial phylogram; radial cladogram. Can also turn the rectangular trees into various orientations. Ladderise left, right or random.
Branch labels: Simple branch labels but only to the right of branches, does not seem to understand BEAST/MrBayes annotations although it supposedly should.
Rooting: Outgroup or midpoint rooting.
Other formatting: Some but more limited than FigTree.
Graphic export: Can export trees as SVG, PDF or various bitmap formats. SVG is good for Inkscape, but if you are using Adobe Illustrator or CorelDraw you might be better served with one of other two tree viewers.
Portability: Available for Windows, Mac or Linux. Have tried the first and the last and both work well.
Other comments: Uniquely, it also offers several interesting analyses of multiple trees such as consensus, tanglegram and networks. Although it is as free as the other two they make you jump through more hoops to get the software.
Verdict: Currently my favourite, mostly because it seems less buggy than the other two and works equally well on both OS I use. Still, it is a bit annoying that I can't get it to do the proper branch labels.