In this example, when an individual reproduces, there is a 50% probability
that a lateral transfer is attempted. If yes, a donor individual is randomly chosen
in the population. A segment of its chromosome is copied and transferred in the
recipient individual (the one which was reproducing). This foreign DNA then replaces
the homologous segment in the recipient chromosome. This is a way to perform allelic 
recombination.

To run this example for 200 generations, type the following commands:
aevol_create
aevol_run_X11 -n 200

Then you can look at all the transfer events that took place by typing:
more log_transfer.out

You can also reconstruct the ancestral lineage of the final best individual and the
mutations that occurred on this lineage, to see whether some transfer events were 
selected:
aevol_misc_lineage -b 0 -e 200
aevol_misc_fixed_mutations -f lineage-b000000-e000200-i...-r...ae 
more stats/fixedmut-b000000-e000200-i...-r...out
 


Details:

A transfer attempt starts by searching for a short region of strong sequence similarity
between the recipient chromosome and the donor chromosome. If none is found, there
will be no transfer. If on the contrary an alignment is found with a sufficient 
score, this initial alignment is extended until there is no sequence similarity 
anymore or until a random event stops the extension -- at each extension step, there 
is a probability called REPL_TRANSFER_DETACH_RATE to stop the extension even if there 
is some sequence similarity. 
