FITS input

FITS requires two types of input: Data file and Parameters file.

Data file

This file is expected to hold observed allele information from the system under study. FITS expects a tab-delimited textual file, with following columns:

1. gen for the generation of the observation
2. allele for the observed state
3. freq for the measured frequency for that state
4. position for the position number for which the frequency data is given (optional)

Note

FITS assumes the columns to appear in the above order.

Note

The allele with the highest frequency at the first available time point will be defined as WT (w=1).

Example data file

gen	allele	freq	position
0	0	1	1
0	1	0	1
1	0	1	1
1	1	0	1
2	0	0.99999	1
2	1	1e-05	1
3	0	0.9999899998	1
3	1	1.00002e-05	1
4	0	0.9999899998	1
4	1	1.00002e-05	1
5	0	0.9999600016	1
5	1	3.99984e-05	1

You can also download an example.

Note

For each generation, the sum of frequencies for the different alleles should be 1.

Note

FITS accepts allele frequencies at a given loci. Sequencing techniques tend to vary in their accuracy, so sometimes the provided allele frequencies may be inaccurate. If using inaccurate input, FITS inferences may be inaccurate as well. Specific examples include:

1. Inference of fitness of highly deleterious mutations where the accuracy threshold of sequencing is worse than the mutation rate.
2. Inference of mutation rate from neutral alleles when the number of generations X the mutation rate is lower than the accuracy threshold of the sequencing.
3. Inference of mutation rate or fitness when very shallow sequencing is available (due to limited sampling or limited sequence coverage).

Parameters file

This file provides FITS with population genetics parameters information of the system under study. Each line in this file represents a different parameter to set, where a space exists between the name of the parameter and its value: <parameter_name> <parameter value>.

Note

If you want to put comments within the parameters file, just add # at the beginning of the comments’ lines.

You can also download an example.

General parameters

Parameter name	Type	Description
N	Integer	Size of population
sample_size	Integer	Size of observed population (e.g., sequenced genomes)
bottleneck_size	Integer	Size of the population transferred on a bottleneck event
bottleneck_interval*	Integer	Number of generations separating between bottleneck events (default: 0)
num_alleles	Integer	Number of alleles observed in all loci
mutation_rateX_Y	Float	Rate of mutation of allele X to allele Y. Not required if mutation rate is to be inferred
fitness_alleleX	Float	Fitness value assigned to allele X. Not required if fitness is to be inferred
logistic_growth*	Float	1: model the population growth throughout the generations with a logistic growth model (default: 0)
logistic_growth_K	Float	Logistic model - upper bound
logistic_growth_r	Float	Logistic model - proportionality constant

*parameter value of 0 means disabled/off; positive values mean enabled/on.

ABC parameters

Parameter name	Type	Description
num_samples_from_prior	Integer	How many simulations to perform
acceptance_rate	Float	Fraction of best simulations to utilize for the inference of the parameter.

Single simulation

Parameter name	Type	Description
num_generations	Integer	Number of generations to simulate
init_freq_alleleX	Float	Initial frequency of allele X

Fitness inference parameters

Parameter name	Type	Description
fitness_prior	Text	One of the following: uniform (for Uniform distribution) log_normal (based on Bons et al. 2018) fitness_composite smoothed_composite (default) See the distribution of the above priors on a (0,2) fitness here
min_fitness_alleleX	Float	The minimum fitness value (inclusive) that may be assigned to allele X
max_fitness_alleleX	Float	The maximum fitness value (exclusive) that may be assigned to allele X

Mutation rate inference parameters

X and Y are alleles defined in the data file (i.e., 0 and 1).

Parameter name	Type	Description
min_log_mutation_rateX_Y	Float	Minimum (inclusive) for mutation rate from alleleX to allele Y
max_log_mutation_rateX_Y	Float	Maximum (exclusive) for mutation rate from alleleX to allele Y

Population size inference parameters

Parameter name	Type	Description
Nlog_min	Float	Minimum (inclusive) exponent for population size
Nlog_max	Float	Maximum (exclusive) exponent for population size