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Remarques sur les révisions

Nom de version : aevol-4.3

Notes de version
New in 4.3:

* The post-treatment view_generation is now functional for 
aevol (with or without space), but not for R-aevol yet. This 
post-treatment is available if X was enabled at the "configure" 
step, which is the case by default.

* Lateral transfer by replacement can now be constrained to 
replace a segment of roughly the same size and sequence as 
the one given by the donor, to simulate allelic recombination. 
To use this kind of transfer by replacement rather than the 
usual one (where the donor and replaced segments only have 
similar sequences at their extremities), add the line 
"REPL_TRANSFER_WITH_CLOSE_POINTS true" in the file. Specifically, a small region of high similarity is 
searched for between the donor chromosome and the 
receiving chromosome. Then 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. Below 
is an example of how to write the file to try for a 
lateral transfer by replacement in 50% of the reproductions, 
with the constraint that the replaced segment must have 
roughly the same size and sequence as the donor segment 
(the last six parameters are for the alignment search): 
WITH_TRANSFER                   true
TRANSFER_REPL_RATE              0.5
ALIGN_MAX_SHIFT         20

* Lateral transfer events by insertion or replacement can be
 logged during the main evolutionary run by adding the line 
"LOG TRANSFER" in the file. They will be written in 
an output file called log_transfer.out.

* Post-treatments lineage and ancstats can replay lateral 
transfer events. To simplify the post-treatments, lateral 
transfer events are treated as mutations and rearrangements. 
They are managed in ae_dna and ae_mutation and no more 
in ae_selection. If RECORD_TREE is set to true and if 
TREE_MODE is set to normal in, the transfer events 
will be saved in the tree files with the transferred sequence. 

* Examples are now provided in the "examples" dir.

Changes in 4.3:

* Replaced most of the --with-xxxxx configure script options 
with --enable-xxxxx.  Supported options for the configure 
script are now [default value in brackets]:
     --with-x                          [yes]
     --enable-optim                    [enabled]
     --enable-raevol                   [disabled]
     --enable-normalized-fitness       [disabled]
     --enable-mtperiod=period          [disabled]
     --enable-trivialjumps=jumpsize    [disabled]
     --enable-devel                    [disabled]
     --enable-debug                    [disabled]
     --enable-in2p3                    [disabled]

* Post-treatment executables are installed into ${prefix}/bin 
rather than ${prefix}/libexec.

Bugs fixed in 4.3:

* Bug #289: Missing lines in the header of stats_bp_best.out

* Bug #293: Initialisation with a clonal population: Individuals
 in the first generation had a rank equal to -1.

* Bug #294: Problems in constructor and copy method of 

* Bug #300: Missing length data in the tree files for the 
rearrangements (NORMAL tree mode).

* aevol_create produced a segmentation fault if did 
not contain a line specifying ENV_AXIS_FEATURES. Now 
this parameter can be omitted, in which case the default value 
would be METABOLISM for the whole x-axis.

* Correction of the default value for the initialisation method, 
which was 0 instead of "ONE_GOOD_GENE | CLONE".

* Correction of memory leaks in the constructor of ae_stats 
and in the destructor of ae_mutation for some mutations.

* Correction of a bug in the lineage post-treatment, which 
would fail after ~1.000 tree files were loaded because the files 
were never closed.