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View Small Subunit rRNA Phylogenies
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Here you can browse, extract subtrees and re-label our Small Subunit rRNA phylogenies through a graphical Java tree viewer, and retrieve the resulting tree in various formats. You can also do the same with an uploaded tree of your own. A further description is available.
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[Note] The tree viewer does not work well on MacIntosh'es; we don't quite know why. It works on MS-Windows, MS-NT (both Navigator and Explorer tested), Linux, SUN Solaris and likely on most other Unix'es. It may not work behind a firewall either.
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[Note] Subtrees generated from this treeview applet will contain branch lengths that are too short. Please don't rely on them until this notice disappears. This does not indicate a problem with the newick trees available on the ftp site.
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Tree View was written by Oliver Strunk and Niels Larsen.
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Trees To View and Extract From
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Select one of the following trees, then choose an output format below. By default you get the Java Tree Viewer.
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[Note] Sequences were included in the release 8.0 trees if the sequence length was >1399 bases AND the percentage of ambiguous bases was <4%. Sequences that do not meet these criteria will be included in subsequent trees. Please see the README file for more information.
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[WNJ] These trees were generated using the WEIGHBOR (Weighted Neighbor Joining) program: William J. Bruno, Nicholas D. Socci, and Aaron L. Halpern. Weighted Neighbor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction, Mol. Biol. Evol. 17 (1): 189-197 (2000).
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[ML] Denotes a tree that was generated using a Maximum Likelihood approach related to that described by Felsenstein (Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368-376). The program used was fastDNAml (Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. 1994. fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. CABIOS 10(1):41-48), which is based on Felsenstein's dnaml version 3.3. The program is available from the RDP FTP server in the programs directory. Additional utility scripts were written by Ross Overbeek.
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Upload Your Own Tree For Viewing (optional)
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If you specify here the name of a treefile on your local machine - use the browse button - then our server will try to load it and display it. The treefile must contain a Newick formatted tree as it is generated by several phylogeny packages, including PHYLIP.
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Select Tree Output Format
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Graphical Tree Interface.
Allows easy selection, collapsing of named groups, creating, changing and deleting node and tip labels, as well as easy creation of subtrees from arbitrary selections. With a good internet connection, the graphical tree should come up in 5-15 seconds, slower with a modem.
Newick Tree Format.
This is the standard nested ASCII tree format read by many phylogeny packages. The bug which left off the ending semicolon of the file has been fixed.
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Results by Electronic Mail
If you have chosen something other than the Graphical Tree View as output and you want to receive the results via e-mail, enter your electronic mail address below.
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Questions? Mail them to RDP-II Support.
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