There are numerous phylogeny viewing programs available, which ones do people use most often? Are there features (e.g., visualisations, data formats, size of tree that can be displayed, annotation) that people feel existing software lack?
I normally use FigTree for a quick and flexible look on phylogenetic data. For small datasets, PHYLIP DRAWTREE or TreeView are enough. But, for printing I really look for some adequate LaTeX package, commonly PSTricks. It's cumbersome but it works and is beautifull, fully customizable. For large trees, some scripting is necessary. But, now there is E.T.E. which is quite handy.
I'm happy to see Rod Page in this forum. Your books on phylogenetics and molecular evolution are part of my everyday life. I do appreciate the effort !!!
I usually do use TreeView. While it may not be particularly new, I think it's stood the test of time well. I've also used Mesquite and some other tools, but I always find myself coming back to TreeView per default.
Among my colleagues, many also use TreeView, so I am sure that if you did put in the effort to update/enhance TreeView, there'd be many who would greatly appreciate it.
Last, but not least: THANK YOU for having produced this gem!
Tried Phyfi]1 for quick trees or iTOL whenever I need that super cool phylogeny tree figure for a publication. I have used TreeView and MEGA earlier. Tried couple of programs from the list of The Phylogeny Tree Drawing / Plotting program from Phylip page.
I really have one main usage for TreeViewX, and that is to quickly visualize a tree from the clipboard when I'm coding. I used TreeView for that previously, but I think I can't run that any more on my new OSX version (10.7 Pussycat or whatever). I vaguely miss the ability to show unrooted trees, which TreeView used to have but the X version doesn't seem to. All in all I find either very handy for this one use case. Other programs (e.g. mesquite) just aren't lightweight and quick enough.
To make a phylogenetic tree one needs a software which makes the tree initially, so I use mega,phylip,molphy to make the initial tree. For making annotations and publication quality trees, I use TreeDyn. For quick visualisation of trees I use these online tools
I like FigTree because it allows me to play with the tree a little bit to mark-up the regions I'm interested in, unfortunately it's Mac OSX only though. Scriptree also seems quite good.
With the availability of larger sequencing data sets I'd like to see tree viewers be able to help distill a phylogenetic tree down to the points of interest. I'd like to be able to use colours and branch grouping to highlight to the reader what I think is relevent.