README PASEX 1.0 Software
Stoeckel Solenn 2013
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To cite this program, Stoeckel & Masson (2013)
Future reference/DOI
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Computes the evolution of genotypic states within a population at one biallelic locus under genetic drift, mutation and partial asexuality after an infinite number of generations using the transition probability between all possible genotypic states. The life cycle involves discrete and non-overlapping generations.

Run PASEX.exe on an x86 or x64 processor using windows or wine (tested on windows 7 and 8). A command-line will ask you for the rate of asexuality, the mutation rate and the population size you want to assess. 

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Input:
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When requested, enter the rate of asexuality (float number using point, between 0 and 1), the mutation rate (float number using point, between 0 and 1) and the population size (an integer number corresponding to the raw number of individuals, no matter identical genotypes or not). Please take care as the number of genotypic state increases exponentially with the number of individuals, and so the transition matrix will need high quantities of RAM (e.g. ~6Go for 140 individuals) and hard drive resources to be stored (e.g. ~2Go for 140 individuals). Check values and press enter to launch the computation.

Output files:
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Two files containing results can be found after the computation in the directory "results", in a subdirectory created to contain those two files. 

- A first file named year-month-day-hour_minute_second PADM N=x1 n=x2 u=x3 Transition Matrix c=x4.txt
  Where PADM strands for Partial Asexuality genetic Drift and 
  Mutation, x1 is the population size, x2 the number of 
  genotypic states (derived from the number of alleles), x3 
  the mutation rate, x4 the rate of asexuality
in which you will find the transition probabilities from each possible genotypic state within a population at generation n to all other possible genotypic states at the next generation n+1 following a multinomial distribution. Genotypic states at generation n are on lines, Genotypic states at generation n+1 are on columns, intersections contain the transition probabilities (from the genotypic state beginning the line at generation n to the genotypic state heading the column at generation n+1).

- A second file named year-month-day-hour_minute_second PADM N=x1 n=x2 u=x3 PopGenIndices c=x4.txt
in which you will find in the three first columns the possible genotypic states of the population, then the corresponding values of allelic identities within population, and between population, then the derived Fis, finally the probability of this genotypic state after an infinite number of generations for the provided rate of asexuality, mutation rate and population size.

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Contact: solenn.stoeckel@rennes.inra.fr Please in email begin the subject by "[PASEX]". Thank you for your cooperation.
