User defined rates (Su)

Su Mode - User-define rates

It is possible to consider that certain lineages evolve at different paces in the species tree and that different gene families can also evolve at different speeds. For this reason, it is possible to include two multipliers. The Species substitution rate multiplier and the gene family substitution rate multiplier.

The number of substitutions taking place in a branch is computed by

Branch length (time) * substitution_rate_multiplier_species * substitution_rate_multiplier_gene_family

To run this, first you need to prepare the rates files:

python RateCustomizer.py S SequenceParameters.tsv ExperimentFolder

This will create two files:

• GT_SubsitutionRates.tsv
• ST_SubsitutionRates.tsv

Then, you can launch the simulation of sequences by running

python Zombi.py Su SequenceParameters.tsv ExperimentFolder