User defined rates (Gu) - thekswenson/Zombi_wiki GitHub Wiki
Gu - User control of genome rates
This mode allows the user to fine control the genome rates. Three additional files are needed. The files are:
Transfer_rates.tsvEvent_rates.tsvExtension_rates.tsv
Watch out, if you try to run the Gu mode before having generated these files, an error message will appear. The files can be generated with the help of the script RateCustomizer. To launch it, just type:
zombiRateCustomizer G Parameters/GenomeParameters.tsv ExperimentFolder
The tree files will be created in the folder ExperimentFolder/CustomRates. You need to modify those files to select the rates per branch for each kind of event before launching the Gu mode by using the command:
zombi Gu Parameters/GenomeParameters.tsv ExperimentFolder
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