Additional Features Mutation File

Additional Hub Correction

Default Value: TRUE

In case of one of the populations in the dataset has a mutation rate significantly higher than the mutations rates of the other populations, the search of paths will be skewed towards that population.

This "switch" will reduce the impact of this dataset feature without completely discard the other populations. Turn off when it is suspected that this could harm the results.

To understand how this correction is performed Click Here.

Frequency Increase Data

Default Value: TRUE

IAMBEE assigns relevance score to each mutation based on its estimated functional impact and/or its relative increase in frequency inside the population during a fitness increase.

To calculate frequency changes for each population the adaptive trajectory is used to delineate selective sweeps, denoted as sudden jumps in fitness or an increase in adaptation depending of the experimental conditions.

The frequency increase of a mutation is equal to the difference in frequency of a mutation before and after the sweep. In case of have just one end-point the parental strain can be used.

Functional-Score Data

Default Value: TRUE

This score reflects how likely a mutation causes a functional change in the resulting proteins.

A suggested way to calculate the functional impact scores for each mutation is by using SIFT scores which are calculated using the SIFT4G-annotator (Click Here).

When this data is not available, turn off this "switch" and do not supply functional score data in the mutation data file.

Any functional impact score measure can be used by IAMBEE, the use of SIFT scores is suggested but not mandatory.
It is important to keep in mind that not all the mutations are directly related to contribute with an adaptive phenotype. To understand how the relevance score assigned by combining the functional impact and/or the frequency increase values is created, follow this Link.