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,
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.