100 1 3 3
1 1 0.75
s m s
5 2 0 1 0 10
1 0 5000
1 0 5000
1 0 5000
1 0 5000
1 0 5000
4 20 100 1 1
3 0 10
3 0 10
3 0 10
3 0 10
1 -3 0 0 0
1 -3 0 0 0
0
0
0
----------------------------------------------------------------------------------------
PopABC - Mark Beaumont & Joao Lopes 01/05/09
>no_iterations, generation_time, no_populations, no_loci
>escalar per locus (autosome - 1; X-linked - 0.75; Y-linked or mtDNA - 0.25)
>type of DNA data (s - sequence; m - microssatelites)
>topology: 0 - uniform distribution;
1 - choose topology from a list;
2 - specify topology manually [e.g. ((Pop1,Pop2)Pop3) -> 1 2 2 3];
3 - uniform distribution (and choose a Model marker);
4 - choose topology from a list (and choose a Model marker);
5 - specify topology manually (and choose a Model marker).
>ne1 params: 1 - uniform distribtuion;
2 - generalized gamma distribution;
>ne2 params
>ne3 params
>neanc1 params
>neanc2 params
>t1 params: 1 - uniform distribtuion;
2 - generalized gamma distribution;
3 - uniform distribtuion (for all time events);
4 - generalized gamma distribution (for all time events);
[for 1 and 2 t(n) is added to t(n+1)]
[for 3 and 4 set only one priors for all t(n)]
>t2
>mig1 params: 0 - no migration;
1 - uniform distribtuion;
2 - generalized gamma distribution;
3 - uniform distribtuion (on number of migrations);
4 - generalized gamma distribution (on number of migrations).
[for 3 and 4 real mig rate is calculated as nmig/Ne]
>mig2 params
>mig3 params
>miganc1 params
>mutM params: 0 - no mutation
1 - lognormal distribution: (mean of mean(log10); stdev of mean(log10);
mean of Sdev(log10); stdev of stdev(log10). Stdev truncated at 0.
2 - normal distribution: (mean of mean; stdev of mean; mean of Sdev;
stdev of stdev. Stdev truncated at 0.
>mutS params:
>recM params: 0 - no recombination;
1 - lognormal distribution: (mean of mean(log10); stdev of mean(log10);
mean of Sdev(log10); stdev of stdev(log10). Stdev truncated at 0.
2 - normal distribution: (mean of mean; stdev of mean; mean of Sdev;
stdev of stdev. Stdev truncated at 0.
>recS params
>migweight: 0 - do not use migweights matrix;
1 - use migweights matrix as following:
0 mw112 mw113
0 mw122 mw123
mw211 0 mw213
mw221 0 mw223
mw311 mw312 0
mw321 mw322 0
, where mwitj is the prob that the fraction of migrantes in pop i comes
from pop j at a period of time before time event t. Sum of prob should
be equal to 1.
[only use migweight if the topology is specified (option 1,2,4 or 5)]
----------------------------------------------------------------------------------------
Tree topology:
|| Neanc2
|| |
t2|| ------------
|| | |
|| Neanc1 |
|| | |
|| | |
t1|| --------- |
|| | | |
|| | | |
\/ Ne Ne Ne
