GP2.7.7.1 (300917): This is the current version. Please note that the program in its current form is no longer maintained.
Some changes has been incorporated ONLY for the viral model under the genepop format. This changes only apply when some selective sites are defined
1) The output is separated in two different files for neutral and selective loci.
2) The population (in generation 0) and sample Gst (last generation) (Nei and Cheser 93 and Wang 15) are computed for the neutral loci.
GP2.7.6 (210317)
1) The random number generator library has changed. Now the random engine and the uniform and normal distributions come from the C++11 random library.
2) Within generations serial sampling has been added. Consult HowTo 19 for more information.
3) The site's selective coefficient, constant or generated by the gamma distribution are now stored and written to file.
GP2.7.5 (240117)
1) Fixed a bug impeding to run the haploid case under a neutral equilibrium simulation model
2) Added the possibility of defining the original sequence. Consult HowTo 11 for more information.
GP2.7.4 (280415)
1) Minor corrections in ms output format
2) The model for the contraction-expansion scenario was improved. Consult HowTo 10 for more information.
3) A parser for optional arguments in the command line has been added. For example the line:
where -path define the path to the program and the input file, in this case the current directory. -inputfile refers to the name of the input file (by default GP2Input.txt) in this case called myinputofGP2.txt. -output is the name of the output directory (default GP2_Results). -fixedseed if true it executes the simulations always with the same seed (default is -fixseed false). -shift refers to the run number in the output file name. By default is 0 and so the first run has output name GP2msout_Run0.txt, the next GP2msout_Run1.txt, etc.
If we use -shift 13 the first run will be GP2msout_Run13.txt, the next GP2msout_Run14.txt and so on. This is useful when running different replicated instances of the same model in different cores in order to get the whole set of output files correctly and sequentially numbered.
GP2.7.3.2 (190315)
1) This update only affects the linux version. Unfortunately, the compilation of the previous version (2.7.3.1) was performed without any optimization directive. This provokes important slowdown in the speed of the executable. New version 2.7.3.2 has been correctly compiled.
GP2.7.3.1 (191213)
1) A bug impeding to run the model of spliting populations when combined with selection at specific sites was fixed.
2) A bug affecting divergent selection for the same -never executed- model combination was also fixed.
3) Minor changes to improve the checking at the input for the splitting model.
GP2.7.3 (021213)
1) The implementation of the independent SNP segregation model has been improved.
GP2.7.2 (230713):
1) Selection under different selective regions was added (see HowTo 18)
2) The implementation of migration timing inside the evolution models is still pending.
GP2.7.1 (090413)
1) Corrected a typo in the reference of GenomePop paper.
2) Corrected a problem with selection when the dominance coefficient was negative.
3) Corrected a problem when combining selection and split of populations in the speciation models.
4) Recombination function for multichromosome cases changed by a more efficient one.
5) User-defined migration flowobjects changed to incorporate timing. This is transparent to the user. The implementation of migration timing inside the evolution models is pending for ver 2.7.2
GP2.7
1) Migration and population size schemes permit now that the population size varies in time (see HowTo 2)
2) Under the full evolution model a minor bug was corrected in order to avoid the occurrence in the same generation of an split and a contraction-expansion.
3) Under multichromosome models there was a problem in the ms-like output regarding the SNP relative positions. Now corrected.
GP2.6.2 (151012): Released on 15 october 2012.
1) A full evolution model has been developed allowing jointly for: Equilibriums, multiple chromosomes, speciation, hotspot recombination, selection and expansion-contraction scenarios.
2) A new output file is generated with the list of substitutions in the whole metapopulation or in isolated populations.
3) The user can input one sequence in fasta format which will be used to initiate the evolutionary process.
GP2.5 (190612): This is a MAJOR UPDATE: Main changes over last version are:
1) Incorporate the various chromosome setting to several models.
2) Some code depuration and improvements.
3) Recombination functions has been checked with a explicit checking function.
GP2.4 (010212): Added arguments to main. First: for input file name, second for output directory.
GenomePop 2.3 (11/11/11): Current version. Changes over last version are: A minor bug affecting only speciation mode. The output format for the divergence value was wrong when more than one sampling was performed. This is fixed now.
GenomePop 2.2 (12/03/11): Main changes over last version are:
1) Possible problem wiht equilibrium with the effective number of alleles (ne). In haploid case: Control if it happens that ne > N then N*(1/ne) < 1 and need to force that each allele occurs at least once in the pop
2) Incorporate the option of haploidy in the computations of ancestral polymorphism values
3) Split processes: Previous version force the split to be equally divided i.e. each new species has N/2 indivs when split occurs. This is generalized now
to allow the split to be N(1/k) and N(k-1)/(k). The number of mutations should be controled also just after split.
GenomePop 2.1.3 (15/02/11): Incorporate computation of ancestral polomorphism in speciation function as:
1) A / TPS(t) = 1 - (NPS(t)/TPS(t))
where TPS(t) are the total number of polymorphic sites at time t and NPS(t) is the number of such sites that are new,
i.e. that doesnt exist in split n-1 given that split n is the last split before time t.
2) A /AcumA where AcumA is the total ancestral variation produced in the history from
the most recent common ancestor
GenomePop 2.1.2 (27/01/11): Incorporate migration options between splitted populations
GenomePop 2.1.1 (26/01/11): The spliting now include the new field "Factor" that multiplies branch length in order to allow ancestral (Factor>1) or recent (Factor<1) radiation.
GenomePop2.1 (07/09/10): Incorporates the splitting of populations.
GenomePop2 beta1 (14/03/10): Incorporates equilibriums. Neutral mutation drift equilibrium (C&K pag323-325): theta = 4Nmu, Efective num of alleles = theta+1. Heterozygote freq=theta/(theta+1)
Homozyg freq is 1/(theta +1). If each allele have equal freq the allele freq is 1/(theta+1). So we compute theta and distribute the theta+1 alleles at freq 1/(theta+1) in pop
Then we use the isf model with the theta+1 selected positions and the corresponding freqs.
(18/03/10):Incorporate the simulation of 10N generations under neutral condition of a
metapopulation of size numpopulations x Kmax just 1 replicate. Afterwards this metapop is divided
in numpopulations and each pop is beginning with this equilibrium in every replicate.
when possible we use scaling (only for the equilibrium computation) in order to
afford computation time. This is done by scaling (reduce Kmax increase mu etc),
perform simulations, estimate genetype frequency and recover the adequate Kmax and distribute
the mutations with the corresponding frequencies.
(20/03/10):
Incorporate the posibility of different selection schemes in different populations
In doing so, nutsit class have added popindex attribute and a matrix selectionpop
is created. The dominace coefficient is constant between populations.
(24/03/10):haplotypes bolean variable is changed to produce additional output with the sampling of
haplotypes (gametes) instead of individuals.
GenomePop 1.0.6e (19/12/09): Relaxed the restriction of frequency <0.5 of inital SNP mutants. The initial mutant frequency under the ifs model can be now any between 0 and 1 (see HowTo 14).
In addition a bug affecting specific nucleotide selection with negative coefficients (s<0), i.e. positive SNP selection, was fixed.
GenomePop2 beta0 (21/02/10): This software evolves from GenomePop v 1.6e to specialize in SNPs i.e. the model JC2 in GP.
It incorporates more output formats than GP 1.6e and selection episodes in user defined time periods. It lost all models
with more than 2 alleles. It also lost models with variable population size (viability model) since the option of contraction-expansions scenarios
already exists.
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 14)
GenomePop 1.0.6c (20/11/09): Fixed a problem with the input file under some Mac systems.
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 1.0.5b (11/08/08): Minor change to update the scaling option in presence of a bottleneck.
GenomePop 1.0.5 (03/08/08): Bottlenecks and population expansion options have been added. A bug affecting the viral model with SNPs was fixed.
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 1.0.4 (17/03/08): Now under the viral model the user can define the percentage of sequence identity.
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 1.0.2 (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 HowTo8).
GenomePop 1.0.1 (08/02/08): Added the possibility of sampling haplotypes (see HowTo7).