Aevol

An in silico experimental evolution platform

Aevol main package

  1. aevol-5

    aevol-5.0.tar.gz1 July 2016556 KB

    Aevol 5, with space, fast wildtype generation and more!

  2. aevol-5-beta8

    aevol-5.0-beta8.tar.gz1 June 2016557 KB

    Preparing for the shiny new Aevol 5

  3. aevol-5-beta6

    aevol-5.0-beta6.tar.gz19 October 2015498 KB

    Preparing for the shiny new Aevol 5

  4. aevol-4.4.2

    aevol-4.4.2.tar.gz13 January 2014519 KB

    Bugs fixed in 4.4.2

    1. Fix compilation error on Mac (tr1 included in std). The new mac compiler includes the tr1 directly in std which caused a compilation error. This issue was specific to aevol-4.4.1

  5. aevol-4.4.1

    aevol-4.4.1.tar.gz9 December 2014522 KB

    Bugs fixed in 4.4.1

    1. Fix abnormally slow graphic output on OSX Yosemite. The OSX Yosemite (10.10) update came with a dramatic slowdown in aevol X displays. The problem comes from slow calls to Xlib functions.

  6. aevol-4.4

    aevol-4.4.tar.gz28 July 2014519 KB

    New in 4.4

    1. aevol_create now gives a name to the created strain. It can be defined using the STRAIN_NAME keyword in the param file. If this keyword is not present, a default one will be generated.

    2. New option -o or --out in aevol_create Allows one to create the experiment in any location.

    3. aevol_propagate can now reset the PRNGs (random generators) with the new general option -S (affecting all random processes) or the new more specific options -m, -s, -t, -e and -n (each affects a single random process, see man page).

    4. The environmental target can be defined by a list of custom points using the ENV_ADD_POINT keyword in the parameter file. This is an alternative to the usual way, where it is defined as a sum of gaussians. Note, however, that environmental variation is possible only for the "gaussian" way.

    5. The aevol_misc_fixed_mutations program now outputs the number of genes affected by each mutation. See the full release notes for more details.

    6. The programs aevol_misc_lineage, aevol_misc_ancstats, aevol_misc_fixed_mutations, aevol_misc_gene_families now work when the environment was changed at some point by aevol_modify.

    7. The fitness proportionate selection scheme now works with spatial structure.

    8. In aevol_modify, it is now possible to replace a population by clones of the best individual. To do so, add the line CLONE_BEST_NO_TREE or CLONE_BEST_AND_CHANGE_TREE in the parameter file you supply to aevol_modify.

    9. New option (-c and -p) in aevol_create. Allows one to load a chromosome (and possibly plasmid) from a text file.

    10. Add a script (src/misc/movies.py) to produce a movie from an aevol simulation with dumps activated.

    11. New program aevol_misc_gene_families: issues the detailed history of each gene family on the lineage of a given individual (providing its lineage file). See the full release notes for more details.

    Changes in 4.4

    1. In aevol_misc_create_eps and aevol_misc_robustness, option -e or --end is now -g or --gener for consistency reasons.

    2. Updated post-treatment template and added it to the compiled sources (so that one can make a new post-treatment with no need to install the autotools).

    Bugs fixed in 4.4

    1. In aevol_create, init_method always set to at least ONE_GOOD_GENE | CLONE, regardless of what was written in the parameter file.

    2. In aevol_misc_lineage, there was a segmentation fault when the population was spatially structured.

    3. aevol_misc_create_eps, was no longer functional since version 4.0.

    4. In aevol_misc_fixed_mutations, the fitness impact of some mutations was wrong if there was some environmental variation.

    5. In aevol_modify, correction of a segmentation fault on change of population size.

  7. aevol-4.3

    aevol-4.3.tar.gz28 January 2014504 KB

    New in 4.3

    1. The post-treatment tools lineage, ancstats and view_generation have been ported to aevol-4

    2. 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.

    3. Lateral transfer events by insertion or replacement can be logged during the main evolutionary run

    Changes in 4.3

    1. Replaced most of the --with-xxxxx configure script options with --enable-xxxxx.

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

    Bugs fixed in 4.3

    1. No major bug was fixed in this version, see the full release notes for minor bugfixes

  8. aevol-4.2

    aevol-4.2.tar.gz10 October 2013467 KB

    New in 4.2

    1. The post-treatment executables are now prefixed with aevol_misc_ and are installed into ${prefix}/libexec rather than ${prefix}/bin.

    Bugs fixed in 4.2

    1. Bugs #281 and #282: Bug in gene position

      This bug happenned whenever a promoter at the end of the genome on the LEADING strand transcribed a gene that was at the beginning of the genome (or a promoter at the beginning on the LAGGING strand transcribed a gene that was at the end of the genome)

      The position of the protein was then out of the genome bound (> genome len when LEADING or < 0 when LAGGING). If this gene was also transcribed on another rna that didn't satisfy the above constraint, it wasn't recognized as the same gene. Either bugs had no effect whatsoever on the fitness and hence on the outcome of evolution. It could however lead to erroneous statistics regarding the number of RNAs a gene is transcribed onto.

    2. Bug #284: Undefined behavior when there is no terminator in the genome

      After a big deletion, it can happen that a genetic unit does not contain any teminator anymore. There can however be a promoter somewhere. The behavior of the program was different depending on the strand where the promoter was. If it was on the lagging strand, the RNA was supposed to be as long as the whole genetic unit, and could carry coding sequences. If the promoter was on the leading strand, the length of the RNA was left as is, that is, either to -1 for generation 0, or to the length inherited from the parent, which made no sense anymore once the terminator has disappeared. We decided that it is best that no RNA is produced in this case (no terminator = incomplete gene, assumed to be non-functional).

    3. Bug #285: "Barrier" events logged twice

      When a deletion would cause the genetic unit to be smaller than the size of a promoter, the mutation was not performed and (if the BARRIER option was chosen in the logs), and the event was logged twice. This kind of mutations is now performed normally (and hence no log entry should be issued) as long as it doesn't make the genetic unit smaller than the minimum length specified (which is independent of the promoter size).

    4. Bug #286: Log files incorrectly regenerated when resuming a run

      When resuming a run, log files are regenerated by copying the header of the former log file and its entries until the generation chosen to resume the run. During this copy, (1) the first entry was skipped, and (2) the entries for the resuming generation were copied, and thus ended up duplicated.

  9. aevol-4.1

    aevol-4.1.tar.gz06 August 2013485 KB

    New in 4.1

    1. Ported the «extract» post-treatment from version 3. This programs can extract from a backup the sequence and the list of all proteins for every individual in an easily parsable text-based format.

    2. aevol_modify allows to modify the axis features and segmentation as well as secretion properties

    3. Added man pages for the 4 main executables

    Bugs fixed in 4.1

    1. Supressed memory leaks.

    2. Introduced in 4.0: Major bias in the spatial competition caused by a bad update.

    3. In aevol_modify, changing environment gaussians was causing a segfault when NOT using environmental variations.

    4. Bug #279: make install no longer fails with error

  10. aevol-4.0

    aevol-4.0.tar.gz24 July 2013511 KB

    New in 4.0

    1. The main aevol executable has been split into 4:

      1. aevol_create: create an experiment with setup as specified in param_file
      2. aevol_run: run a simulation
      3. aevol_modify: modify an experiment as specified in param_file
      4. aevol_propagate: create a fresh copy of the experiment

Older versions

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