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  • Nemo – A stochastic, individual-base, genetically explicit simulation platform

Nemo – A stochastic, individual-base, genetically explicit simulation platform

http://nemo2.sourceforge.net/index.html
  • recombination map has been added for all multi-locus traits. The map positions (chromosomal) for neutral markers (e.g. SNPs) and loci under selection (QTLs, deleterious mutations, DMIs) can now be specified explicitly, or set at random. The map can hold an unlimited number of loci of different types jointly, at any recombination scale (cM or lower). The effects of linkage can thus be finely explored.

  • A new trait coding for (Bateson-)Dobzhansky-Muller incompatibility loci. Multiple haploid or diploid pairs of incompatible loci can be spread throughout the genome and affect individual fitness.

  • Multi-type selectionIndividual fitness can be jointly determined by different types of loci under selectinon, such as QTLs coding for quantitative traits under spatially variable selection, universally deleterious mutations, and Dobzhansky-Muller incompatibility loci.

  • An unlimited number of quantitative traits under different forms of selection can be modelled, based on universally pleiotropic loci with several bi- or multi-allelic models.

  • Spatial and temporal variation of selection on quantitative traits is possible, modelling shifts of environmental conditions over time.

  • The dispersal matrix describing the movement of individuals among sub-populations can be replaced by a connectivity matrix and a reduced dispersal matrix describing migration only among the connected sub-populations. This offers a substantial gain in computing time and system memory when simulating very large grids.

  • Input parameters' arguments may be specified in separate files. This is particularly convenient when specifying large matrices.

  • Many adjustments have been made for refined control of the input of parameters and data output. See updates in the manual.