User defined rates (Gu)

Gu - User control of genome rates

This mode allows the user to fine control the genome rates. Three additional files are needed

• Transfer_rates.tsv
• Event_rates.tsv
• Extension_rates.tsv

The files can be generated with the help of the script RateCustomizer. To launch it, just type:

python RateCustomizer.py G ./Parameters/GenomeParameters.tsv ExperimentFolder

The tree files will be created in the folder ExperimentFolder/G/Rates. You can modify those files to select the rates per branch for each kind of event:

Transfer_rates.tsv

The first column corresponds to the donor, the second column corresponds to the recipient, and the third column corresponds to the weight that the connection between the two has. When a transfer event takes place, the donor searches for all the possible candidates and it will transfer a given gene with a probability proportional to the weight of the candidate. This is an easy way to model transfers that are forbidden between some pairs (it suffices to give a weight of 0 to the couple) or highways of transfers

Event_rates.tsv

Each line corresponds to a node of the species tree. The different column correspond to the branch-wise rates for the different events

• Extension_rates.tsv

Similar to the previous file, but with the values for the extension parameters

To launch this mode, then simply write

python Zombi Gu GenomeParametersFile.tsv ExperimentFolder

The rates will be read from the files just generated. Watch out, if you try to run the Gu mode before having generated those files, an error message will appear