Specifying a model

Related options

Please read more about Theta0 and Mutation rate here.

Types of demographic models

GADMA could infer two base types of demographic models:

Demographic model with structure (up to 3 populations). It is a more flexible model type as dynamics of population size change could be inferred and it has a lot of options for parameters.

Related options

Base options:
- Initial structure
- Final structure (optional)
Additional options:
- Only sudden fixes constant population sizes instead of dynamics inference.
- No migrations disables all migrations.
- Symmetric migrations makes all migrations symmetric.
- Migration masks enables/disables migrations selectively.
- Split fractions infers fractions in which ancestral population is split.
- Inbreeding infers inbreeding coefficients (only for dadi engine).
- Selection infers selection coefficients.
- Ancestral size as parameter disables multinomial approach of dadi and moments engines when ancestral size is inferred implicitly.
- Lower bound of first split limits lower bound of the most ancient split.
- Upper bound of first split limits upper bound of the most ancient split.
- Lower bound of second split limits lower bound of the next to the most ancient split.
- Upper bound of second split limits upper bound of the next to the most ancient split.

Custom demographic model. It is a usual user-specified model like in dadi, moments and other tools for demographic inference. Using such a model will give more control over parameters and could be used for inference of more than 3 populations but is less flexible.

Related options

Base options:
- Custom filename - path to file with specified demographic model.
Additional options:
- Lower bound - list of lower bounds for model parameters.
- Upper bound - list of upper bounds for model parameters.
- Parameters identifiers - names/identifiers of the parameters.