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