cluster

• Introduction
  • Flow Diagram
• Overview of Parameters
• Details to Parameters
  • --genome
  • --N
  • --rr
  • --nsmodel
  • --cluster
  • --basepop

Introduction

Flow Diagram

At each generation Invade-cluster proceeds in the following order

Overview of Parameters

Following an overview of the parameters. Detailed descriptions for more complex parameters are provided in the next section

** Mandatory parameters**

• --genome: specify the properties of the simulated genome (for details see next section)
• --u the transposition rate, i.e. the propability that a TE insertion is generating a new one
• --N: the population size (in diploids)
• --gen: the number of generations to simulate
• --basepop: specify the distribution of insertions in the starting population (for details see next section)

Optional parameters

• --rep the number of replicate runs to use
• --rr the recomination rate (for details see next section)
• --cluster the size of piRNA clusters (for details see next section)
• --uc the transposition rate with at least one insertion in a piRNA cluster; default=0.0
• --v the excision rate
• --vc the excision rate with at least one insertion in a piRNA cluster
• --x the negative effect of a TE insertion; default=0.0
• --t the degree of epistatic interactions between TEs; default=1.0 (no interactions)
• --steps store the output each --steps generation
• --nsmodel negative selection model (for details see next section)
• --seed a seed for the random number generator (allows reproducing previous results); default = current time
• --min-w minimum fitness; a population will die out if fitness drops below --min-w
• --detailed-output-file: a file for detailed output such as the SFS of TEs, or the insertion counts for every individual in the population
• --sim-id simulation id; maybe useful for plotting the results in R with ggplot2; especially if multiple independent simulations were performed
• --tally-file optional output of the number of TE insertions per diploid individual;
• --sfs-file the site frequency spectrum
• --mhp-file optional output of the position and population frequency of TE insertions; allows to generate Manhattanplots about the landscape of TE insertions
• --silent do not show log (just show output) actually recommended
• --help display help

Details to Parameters

--genome

Specify the genome, following some examples

• '--genome Mb:1' simulate a single chromosome of size 1 million base pairs
• '--genome Mb:1,2,1,4' simulate four chromosomes with sizes 1, 2, 1 and 4 million base pairs
• '--genome kb:34,15' simulate two chromosomes with size 34 and 15 thousand base pairs
• '--genome bp:1000,5000' simulate two chromosomes with size 1000 and 5000 base pairs
• '--genome 1000,2000' simulate two chromosomes with size 1000 and 2000

Note the unit is optional, if not provided a default unit of bp is assumed

--N

Specify the population size; This is a mandatory parameter. Following some examples

• '--N 500' a population size of 500 will be used
• '--N 0:500, starting at generation size 0 a population size of 500 will be used (same as '--N 500'); generation zero is the base population
• '--N 0:500,1000:2000' from generation 0 to 1000 a population size of 500 will be used; Starting at generation 1000 a population size of 2000 will be used
• '--N 0:300,40:500,100:1000' from generation 0 to 40 a population size of 40 will be used; from generation 40 to100 a population size of 500 will be used; starting at generation 100 a population size of 1000 will be used
• --N 40:500,100:1000,0:300,' from generation 1 to 40 a population size of 40 will be used; from generation 40 to100 a population size of 500 will be used; starting at generation 100 a population size of 1000 will be used;

Note the order of the generations is not important (compare with prev. example)

Note a population size for the base population must be provided

--rr

Provide the recombination rate. This is an optional parameter. A default recombination rate of zero will be used when not provided.

Following some examples

• '--rr lambda:2' simulate a mean number of cross overs of 2 for one chromosome
• '--rr lambda:2,3,2,1' simulate a mean number of cross overs of 2 for the first chromosome, 3 for the second, 2, for the fourth and 1 for the fifth.
• '--rr cm_mb:4' simulate a cross over rate of 4 centiMorgan per megabase pair for the first chromosome
• '--rr cm_mb:4,2,10' simulate a cross over rate of 4 centiMorgan per megabase pair for the first chromosome, 2 for the second and 10 for the third

Note the number recombination values must match the number of chromosomes
Note if this parameter is not provided a recombination rate of 0.0 will be used for all chromosomes

--nsmodel

Model of negative selection against TEs. Three possible models are supported

• '--nsmodel add' additive effects; each insertions contributes equally to fitness. Consequently homozygous insertions count as two.
• '--nsmodel het' only heterozygous insertions contribute negatively to fitness. This is justified by ectopic recombination
• '--nsmodel rec' recessive model; only homozygous insertions contribute to fitness; Justified by haplosufficiency

--cluster

The sizes of piRNA cluster; If not provided no piRNA clusters are simulated. A different size may be provided for each chromosome.

Note if piRNA-clusters are used, the number of chromosomes must match the number of piRNA clusters; If a chromosome does not have a piRNA cluster provide a size of zero.

• '--cluster 100' the first chromosome has a piRNA cluster of size 100bp (in conjuction with e.g. '--genome kb:1)
• '--cluster 0,0,100' the third chromosome has a piRNA cluster of size 100bp (in conjuction with e.g. '--genome kb:1,2,1)
• '--cluster 0,0,100' the third chromosome has a piRNA cluster of size 100bp (in conjuction with e.g. '--genome kb:1,2,1)
• '--cluster 200,100' the first chromosome has a piRNA cluster of size 200bp and the second of size 100bp (in conjuction with e.g. '--genome kb:1,2)
• --cluster kb:0.5,0.2' the first chromosome has a piRNA cluster of size 500bp and the second of size 0.2kb
• '--cluster 0,0,0,1000'
• --cluster Mb:0.5,0,0,1'

--basepop

Define insertions in the starting population. Following some examples

• '--basepop seg:50' will simulate 50 segregating insertions with random positions; All insertion will have the population frequency of 1/2N (unless due to chance two or more insertions occur at the same site)
• '--basepop fix:10' will simulate 10 fixed insertions with random positions