This directory (bestfit) contains an example of the use of the cosi
simulation, implementing the calibrated model for three human
populations published in Genome Research (currently in press).  The
script "run.pl" runs both the program for generating a random local
recombination map ("recosim") and the coalescent program itself
("coalescent").  "recosim" is controlled by the parameters in the file
"recParams"; "coalescent" is controlled by the parameters in the file
"params".  See the documentation directory for definitions of the 
parameters.  The only other thing "run.pl" does (besides calling the two
programs) is extract the sequence length to be simulated from the
params file, to guarantee that the two programs use the same length.

"recosim" outputs the recombination map in the file "model.test" (the
name is set as a parameter in "recParams").  The regional
recombination rate is picked from a distribution found in
"autosomes_deCODE.distr" (which is, not surprisingly, the distribution
seen in the deCODE genetic map for the autosomes).

In this example, the parameter file for coalescent is "params".  It
sets things like the mutation rate, gene conversion rate and sequence
length.  (With this model, sequences up to ~1 Mb generally run in a
reasonable time, provided the extreme tail of the recombination rate
is truncated -- see program documentation.) It also defines the sampled
populations, their effective population size (in the present) and the
number of sampled chromosomes.  The rest of the file defines the
demographic history of the popualations -- in this case, an
Out-of-Africa model of an ancestral population that splits into
Africans and non-Africans, and then into Europeans and Asians; African
Americans are modeled as a recent admixture of the African and
European populations.


