Question: What Is A Good Phylogenetic Tree Viewer, Such That I Can View Internal Nodes?
2
gravatar for Lee Katz
10.0 years ago by
Lee Katz3.1k
Atlanta, GA
Lee Katz3.1k wrote:

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.

ADD COMMENTlink modified 7.2 years ago by Istvan Albert ♦♦ 86k • written 10.0 years ago by Lee Katz3.1k

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

ADD REPLYlink modified 16 months ago by _r_am32k • written 10.0 years ago by lh332k

I use seaview, ete2 and iTol.

ADD REPLYlink written 7.2 years ago by Pappu1.9k
3
gravatar for Jorge Amigo
10.0 years ago by
Jorge Amigo12k
Santiago de Compostela, Spain
Jorge Amigo12k wrote:

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.

ADD COMMENTlink modified 7.2 years ago by SES8.4k • written 10.0 years ago by Jorge Amigo12k

+1 for Archaeopteryx.

ADD REPLYlink written 10.0 years ago by lh332k

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

ADD REPLYlink written 10.0 years ago by Lee Katz3.1k

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

ADD REPLYlink written 7.2 years ago by SES8.4k
1
gravatar for Michael Dondrup
9.9 years ago by
Bergen, Norway
Michael Dondrup48k wrote:

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.

ADD COMMENTlink written 9.9 years ago by Michael Dondrup48k
0
gravatar for Larry_Parnell
9.9 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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.

ADD COMMENTlink modified 7.2 years ago by Istvan Albert ♦♦ 86k • written 9.9 years ago by Larry_Parnell16k
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