Centroid Wheel Tree

Centroid Wheel Tree is an Intuitive, Informative, and Most Balanced representation of phylogenetic trees.

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Contact

Wataru IWASAKI
Dept. Biological Sciences,
Grad. Sch. Science,
University of Tokyo, Japan
E-mail:
iwasaki AT bs.s.u-tokyo.ac.jp

Licenses

CWT Software:
GNU General Public License
The other content:
Creative Commons License

How to Prepare Input Data

To create wheel trees, you need to input a group of candidate phylogenetic trees.
You can prepare such trees by manually gathering trees created using different methods or by conducting statistical phylogenetic tree estimation.

If you have just sequences and are not so familiar with computational analysis, an on-line phylogenetic analysis service Phylogeny.fr would help you much.
For example, to obtain bootstrap trees with the neighbor-joining method,

(1) Visit Phylogeny.fr
(2) Choose "MUSCLE", "Gblocks", and "ProtDist/FastDist + Neighbor" for the Multiple Alignment, Alignment Curation, and Phylogenetic Tree Construction methods, respectively.
(3) Unmark "Visualisation of phylogenetic tree".
(4) Click "Create workflow".
(5) Paste your sequences to the box appeared.
(6) Enter an arbitrary number to "Number of bootstraps" box in the "Phylogeny: Neighbor" section to invoke bootstrap analysis.
(7) Adjust other settings if necessary and click "Submit". Then, the phylogenetic analysis starts.
(8) After the analysis finishes, click "List of bootstrap trees in Newick format" and save the candidate tree file, which can be directly used as CWT input.

On the other hand, you may conduct phylogenetic analysis on your own computers.
For example, if you use PHYLIP, you can convert the SEQBOOT output to distance matrices by using DNADIST or PROTDIST and use the neighbor-joining tree reconstruction program NEIGHBOR.
Then, you will obtain an "outtree" file, which can be directly used as CWT input, instead feeding it into the CONSENSE program.

A maximum-likelihood program RAxML also provides a bootstrap tree file (RAxML_bootstrap.***), which can be used as CWT input.

You may also use other phylogenetic estimation programs.
Note that, since some of such programs discard intermediate candidate trees, in some cases you might need to write scripts to retrieve such trees.
For example, you need to conduct tree estimation in parallel for each bootstrap alignment created by PHYLIP SEQBOOT, instead of using built-in bootstrapping functions.