1000 20 5 3
1 1 0.75
m s m
0
1 0 1000
1 0 1000
1 0 1000
1 0 1000
1 0 1000
1 0 1000
1 0 1000
1 0 1000
1 0 1000
3 0 100000
1 0 0.01
1 0 0.01
1 0 0.01
1 0 0.01
1 0 0.01
0
3 1 1
0
1 -3.18 0.05 0 0
1 -4.18 0.05 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 mitDNA - 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
>ne4 params
>ne5 params
>neanc1 params
>neanc2 params
>neanc3 params
>neanc4 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 params
>t3 params
>t4 params
>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
>mig4 params
>mig5 params
>miganc1 params
>miganc2 params
>miganc3 params
>mutM params: 0 - zero 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 - zero 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 mw114 mw115
0 mw122 mw123 mw124 mw125
0 mw132 mw133 mw134 mw135
0 mw142 mw143 mw144 mw145
mw211 0 mw213 mw214 mw215
mw221 0 mw223 mw224 mw225
mw231 0 mw233 mw234 mw235
mw241 0 mw243 mw244 mw245
mw311 mw312 0 mw314 mw315
mw321 mw322 0 mw324 mw325
mw331 mw332 0 mw334 mw335
mw341 mw342 0 mw344 mw345
mw411 mw412 mw413 0 mw415
mw421 mw422 mw423 0 mw425
mw431 mw432 mw433 0 mw435
mw441 mw442 mw443 0 mw445
mw511 mw512 mw513 mw514 0
mw521 mw522 mw523 mw524 0
mw531 mw532 mw533 mw534 0
mw541 mw542 mw543 mw544 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:
|| Neanc Neanc Neanc
|| | | |
t4|| -------- ---------- -----------
|| | | | | | |
|| Neanc | | Neanc Neanc |
|| | | | | | |
t3|| -------- | | ------- --------- |
|| | | | | | | | | |
|| Neanc | | OR | | Neanc OR | Neanc |
|| | | | | | | | | |
t2|| ------- | | | | ----- | ----- |
|| | | | | | | | | | | | |
|| Neanc | | | | | | | Neanc | | |
|| | | | | | | | | | | | |
t1|| ----- | | | ----- | | | ----- | | |
|| | | | | | | | | | | | | | | |
\/ Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne
