仅作个人笔记使用意思就是只考虑我能不能看懂
只谈两个群体
配置文件来自于fsc论坛
https://groups.google.com/g/fastsimcoal/c/AKrFl7v0Ft0
适用于最新版本的fsc-
模型是这样的:
early gene flow tpl文件
I think you can simplify your tpl file. Maybe try something like:
//Parameters for the coalescence simulation program : fastsimcoal.exe
2 samples to simulate
//Population effective sizes (number of genes)
CAPOPSIZE
JUPOPSIZE
//Haploid samples sizes
10
10
//Growth rates: negative growth implies population expansion
0
0
//Number of migration matrices : 0 implies no migration between demes
3
//Migration matrix 0
0 0
0 0
//Migration matrix 1
0 M23
M32 0
//Migration matrix 2
0 0
0 0
//historical event: time, source, sink, migrants, new deme size, new growth rate, migration matrix index
3 historical event
Tmig 0 0 0 MID1 0 1 absoluteResize
Tmig 1 1 0 MID0 0 1 absoluteResize
TDIV 0 1 1 ANCPOPOSIZE 0 2 absoluteResize
//Number of independent loci [chromosome]
1 0
//Per chromosome: Number of contiguous linkage Block: a block is a set of contiguous loci
1
//per Block:data type, number of loci, per generation recombination and mutation rates and optional parameters
FREQ 1 0 3.03e-9 OUTEXP
- est文件
For the est file I'd advice to use loguniform distribution for large search ranges
// Priors and rules file
// *********************
[PARAMETERS]
//#isInt? #name #dist.#min #max
//all Ns are in number of haploid individuals
1 CAPOPSIZE logunif 1e2 1e8 output
1 JUPOPSIZE logunif 1e2 1e8 output
1 ANCPOPOSIZE unif 1e2 1e8 output
1 MID0 logunif 1e2 1e8 output
1 MID1 logunif 1e2 1e8 output
1 Tmig unif 1 1340000 output bounded
1 TDIV unif Tmig 1340000 output paramInRange
0 M23 logunif 1e-7 1 output
0 M32 logunif 1e-7 1 output
[COMPLEX PARAMETERS]
