This page gives an overview of the algorithm used by Featurama. For more in depth explanations and information about data structures used in Featurama see Development Pages.

1. Featurama0.7 starts by either processing a config file if one was specified or asking the user to set a series of paramaters.
2. After the parameters have been set Featurama0.7 begins searching for features by first processing the input FASTA file and then applying the algorithm shown on this flow chart with the specifed parameters.
3. As the parameter search is happening Featurama0.7 verifies that every feature it chooses is unique among all the features it has chosen. If a feature found at one stage in the search is found to contain a duplicate, the feature is deleted from the gene for which it was found, and the gene is searched for another feature as long as the search parameters permit.