GenomePop 1.0.1 (08/02/08): Added the possibility of sampling haplotypes (see HowTo section, point 11).
GenomePop 1.0.2 (16/02/08): The algorithm for SNPs recombination has been highly improved (hotspot improvement is pending).
The management of independently segregating SNPs is now explicitly allowed (see HowTo section, point 12).
GenomePop 1.0.3 (28/02/08): Bug on JC2 (SNP model) recombination fixed. Bug on variable population size evolution
affecting the non neutral model, fixed. Bug fixed and change in intracodon recombination to avoid the generation of stop codons.
The possibility (user-defined) of ignoring intracodon recombination under codon models added.
GenomePop 1.0.4 (17/03/08): Now under the viral model the user can define the percentage of sequence identity (see HowTo section, point 14)
GenomePop 1.0.4b (19/05/08): Minor changes to protect against problems in random seed generator and to improve speed under linux OS.
GenomePop 1.0.5 (03/08/08): Bottlenecks and population expansion options have been added. Also the possibility of storing the root sequence (see HowTo section, points 15 and 16). A bug affecting the viral model with SNPs was fixed.
GenomePop 1.0.5b (11/08/08): Minor change to update the scaling option in presence of a bottleneck.
GenomePop 1.0.6 (14/02/09): Fixed a bug in JC2 models with site selection causing non sampling i.e. the whole population was been returned.
Fixed a bug in the binary recombination function (JC2 models) causing less recombination than should be.
Beneficial mutation added: In models with constant N just put negative s. For models with variable N the initial fitness
should be less than 1 in the case of beneficial mutations. In models with N variable the parameter Rmax is min{3, ceil(1/initialfitness)}.
Changed the algorithm for binary recombination in JC2 models because poor efficiency of the previous one in some cases. Change in default parameters.
Now diploidy is assumed by default.
GenomePop 1.0.6c (20/11/09): Fixed a problem with the input file under some Mac systems.
GenomePop 1.0.6d (27/11/09): This version is a pre-release of v 1.0.7 just incorporating the possibility of defining mutations at a given frequency in specific positions and populations (see HowTo 17)
GenomePop 1.0.6e (19/12/09): Relaxed the restriction of frequency <0.5 of inital SNP mutants. The inital mutant frequency under the ifs model can be now any between 0 and 1 (see HowTo 17).
In addition a bug affecting specific nucleotide selection with negative coefficients (s<0), i.e. positive SNP selection, was fixed.
In preparation GenomePop 1.0.7: Different spatial (interpopulation) and temporal selection schemes and equilibrium burn in.