EVOLGENIUS 5.6 OUTPUT FILE

The real value of Evolgenius is the excel file produced at the end of a set of simulations. All of the program settings are reported on the first worksheet (labeled "Initial Settings").

The results of individual iterations are reported on the next worksheet (labeled "Iterations").



Finally, summary information is reported.



Explanation of the Iterations worksheet.

• Iteration. This Identifies the iteration. This is useful if an iteration goes extinct, in which case the iteration number will be skipped in the table.
  
  
• Gens Complete. This reports the number of generations completed for the iteration. Depending on the settings, this value may or may not exceed the fixation times of alleles and gene copies.
  
  
• Gene Alpha Data.
  • Allele of Gene Alpha Fixed. If either the A or a allele fixes, the fixed allele is reported. Note: this value is reported whenever an allele fixes, in accordance with the settings chosen by the user. It does not automatically mean that the frequency of the fixed allele is 1.0 at the end of the simulation, since mutation may re-introduce the other allele.
    
    
  • Gens to Fix Gene Alpha Allele. If either the A or a allele fixes, the generation at which fixation occurred is reported.
    
    
  • Final f(A). The frequency of the A allele at the end of the iteration is reported.
    
    
  • ID# of Gene Alpha Copy Fixed (MRCA). If at some point in the iteration every copy of gene Alpha can be traced back to a single common ancestor at Generation 0, the position in the original data array of the fixed Alpha gene copy is given. This information is mainly used for quality assurance.
    
    
  • Gens to Fix Gene Alpha Copy. If at some point in the iteration every copy of gene Alpha can be traced back to a single common ancestor at Generation 0, the number of generations required for gene copy fixation is reported.
    
    
  • Haplotype from which Fixed Alpha Copy Arose. If at some point in the iteration every copy of gene Alpha can be traced back to a single common ancestor at Generation 0, the haplotype with which the copy was originally associated is reported.
    
    
  • Genotype from which Fixed Alpha Copy Arose.If at some point in the iteration, every copy of gene Alpha can be traced back to a single common ancestor at Generation 0, the genotype with which the copy was originally associated is reported.
  
  
  
• Gene Beta Data. See above and substitute "Beta" for "Alpha."
  
  
• Final Genotype Frequenies. The final frequencies of the ten possible genotypes (i.e., pairs of haplotypes) are reported. Note that there are two possible genotypes for AaBb: AB/ab and Ab/aB.
  
  
• Final Haplotype Frequencies. The final frequencies of the four possible haplotypes are reported. These data are especially useful for analysis of linkage disequilibrium.
  
  

Explanation of the Statistics Table

• Fixation Times. The mean, standard deviation and standard error of fixation times are reported. In some cases (e.g., very large numbers of iterations), this is automatically disabled.
  
  
• Number of Fixations. The number of times the upper- and lower-case alleles fixed are reported, as well as the number of times the population went extinct.