What Is A Good Phylogenetic Tree Viewer, Such That I Can View Internal Nodes?

Question

[Lee Katz]

What is a good phylogenetic tree viewer, such that I can view internal nodes? I have run a script to name internal nodes according to their descendants. My goal is to find internal nodes with homogeneous descendants. I would like to do this by eye but the phylogenetic tree viewers I have tried do not have options, or at the least obvious options, to display these internal node names. I have already tried Mega, Dendroscope, and DNAstar. Any other options?

Alternatively, does anyone have a good script to collapse a large (N>1500) tree according to the leaves naming scheme? My end goal is to cluster the tree as best as possible automatically. Thank you.

[lh3]

This thread As Dendroscope does not work for you, try FigTree and Archaeopteryx.

[Pappu]

I use seaview, ete2 and iTol.

Answer 1

[Jorge Amigo]

tree viewers have been discussed around here a few times before, so you can even try browsing BioStar for such information. my personal option, and I should say that I'm not a phylogenetic-centered bioinformatician, would be Archaeopteryx (what a name!), the successor to ATV based on the forester libraries. it is the sugested interface for the phyloxml syntax, which I have found great to represent any tree I have had to deal with.

[lh3]

+1 for Archaeopteryx.

[Lee Katz]

It worked, thanks! I can view internal node names now.

[SES]

I fixed the link to Archaeopteryx, which was no longer working.

Answer 2

[Michael]

Have a look at Epos, it is a Java library and application that can do a lot of weird things with phylogenies, multiple alignments and trees. Among other things it can display a tree with inner node labels. The search function allows to search for all node names and matching subtrees can be highlighted. If it can handle a large tree like yours could be worth a try.

Answer 3

[Larry_Parnell]

See this What phylogeny viewing software do you use? . It asks a similar question and/or the links provided therein could allow you to do what you need. I would also look at the links provided in Roderic Page's blog, iPhylo. Phyloviewer and Topiary Explorer are two viewers that you should check.