To start a new analysis go to the Run Analysis page, where you can select one or more samples by using the search bar on the left. Once you have a set of samples selected, just select an analysis to perform on the right and click "Run".
In order to start a whole-genome alignment, type the name of the organism in the text bar in the Alignments section. You may enter the name or numeric taxonomic ID associated with any organism in the One Codex Database.
Some of the analyses on this page come at an additional cost, which require that you have payment information on file.