SLiM 3.1 released

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Ben Haller

Sep 3, 2018, 6:03:56 PM9/3/18
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We have just released SLiM 3.1.  It contains a few important changes:

- Spatial interactions are often much faster, especially in models using a large population size.  The speedup may be an order of magnitude or more, for interaction-intensive models.  Several new methods have been added to InteractionType to provide additional functionality.

- Tree-sequence recording is considerably improved under the hood.  The rememberIndividuals() method now actually remembers individuals (not just their genomes), constructing a neutral burn-in history for models using the coalescent is now possible with "recapitation" (see the new recipe 16.10), and many smaller details have been improved and cleaned up.

- Recipe 13.4 (reading MS format files) has been sped up enormously, and a new recipe (section 13.19) has been added showing how to model biased gene conversion in SLiM.

- A few fixes for bugs which you are unlikely to have seen (you would have noticed :->).  As always, further details on the release can be found in the revision history in the SLiM manual.

This version is recommended for all users, but if you are using spatial interactions or tree-sequence recording, you will find this update particularly important and beneficial.

Reproducibility and compatibility: SLiM 3.1 may break backward reproducibility for some models (i.e., the same model, with the same seed, may produce different results than it did in SLiM 3.0).  It should be almost entirely backward compatible with SLiM 3.0, in the sense that changes to your model script should generally not be necessary; the major exception is that some uses of the strength() method of InteractionType may need to be changed because the first argument is now required to be singleton.  If you have saved .trees files from SLiM 3.0, they will not be usable in SLiM 3.1; your .trees output files will need to be re-generated due to large changes under the hood in the .trees file format.  If you are using .trees files, you will probably also want to upgrade to msprime 0.6.1 and pyslim 0.1 at the same time updating to SLiM 3.1.

You can obtain SLiM 3.0 from the SLiM home page at; note that the manuals, recipes, and reference sheets have also undergone revisions.

If you have any questions, comments, etc., please use the slim-discuss group for that.  Thanks, and happy modeling!

Benjamin C. Haller
Messer Lab
Cornell University
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