SLiM 3.3.1 released

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Ben Haller

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Sep 28, 2019, 5:06:41 PM9/28/19
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Hi everyone.  We have just released SLiM 3.3.1.  This is a minor release, with a couple of small feature additions:

- the clock() and executeLambda() Eidos functions now support a real-time monotonic clock as well as a CPU-time clock

- the system() function now has a wait=T optional parameter; if it is set to wait=F the system call will execute in the background

- the Genome class now has a property named individual, to get the individual the genome belongs to

There are a couple of significant bugs found and fixed:

- if genomic elements are specified out of sorted order, *and* a non-uniform mutation rate map is supplied, incorrect results could be generated; some genomic elements might not generate mutations at all

- blank lines could occur in nucleotide-based output when output of back-mutations was suppressed with simplifyNucleotides=T

- recipes involving re-seeding the random number generator now generate a new seed up to 2^62 instead of 2^32, avoiding issues with repeating random number sequences; any models that used the old 2^32 strategy should be updated to use 2^62 instead for safety

The other bugs fixed were crashes in various unusual circumstances; if you hit them you know it :->, otherwise you are unlikely to have been affected by them.

This upgrade is recommended for all users, since it fixes several bugs and does not involve destabilizing changes elsewhere in the code.  This release preserves backward reproducibility (i.e., the same model, with the same seed, will produce the same results as SLiM 3.3, apart from the bugs fixed) and backward compatibility (models that ran under SLiM 3.3 should not require changes to their code).

You can obtain SLiM 3.3.1 from the SLiM home page at http://messerlab.org/slim/; note that the manuals, recipes, and reference sheets have also undergone revisions.

If you're a beginner in SLiM, you might want to check out our recent paper "Evolutionary modeling in SLiM 3 for beginners" (http://dx.doi.org/10.1093/molbev/msy237).

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

Benjamin C. Haller
Messer Lab
Cornell University

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