Nemo Files

N E M O v2.4.0 [22 May 2026]

Latest release.

Please report issues to https://groups.google.com/g/nemo-simul.

We have made major changes in the quantitative trait and overall performances,
thanks to bit encoding of all di-allelic genetic elements (quanti, dmi, delet,
ntrl markers).

The quantitative trait has been enhanced with options to modify the degree of
pleiotropy among loci. Now, quantitative loci can vary in their pleiotropic
degree from no pleiotropy (affect one trait) to full pleiotropy (affect all
traits). The mutation matrix can thus be locus-specific.

The multi-linear model of epistasis for quantitative trait loci has also been
added, allowing for non-linear genotype-phenotype mapping of the quantitative
traits. Epistasis does not vary with pleiotropy (no epistatic pleiotropy).
Epistatic networks can be specified with the quanti_epistatic_network parameter.

A new LCE is introduced: "phenotype_expression". It models phenotypic plasticity
of the quantitative trait with a linear reaction norm. The LCE is linked to
the quantitative trait. Multiple quantitative traits can be plastic with evolving
norms of reaction (intercept and slope can evolve).

New selection models are available: linear, disruptive, and truncation, in
addition to the existing Gaussian and quadratic models. A shared offset parameter
allows fine control of the fitness landscape. Trait index mapping in
selection_trait_dimension enables selecting on a subset of quantitative traits.

Diallelic neutral loci can now be encoded as bitstrings for improved performance,
alongside the existing byte encoding. Hardware POPCNT is used when available.

Recombination of multiple traits on the same genetic map has been revised and
optimized, which reduces run time for large maps (large number of genetic
elements on the same map).

We added more options for and optimized reproduction in Wright-Fisher populations.

Many bugs have been fixed by revising large parts of the code.