Getting started

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Genetic genealogy

1	Getting started
2	Main menu
3	Displaying the results
4	Creating and editing a pedigree
5	Tuning accuracy
6	What does the progress bar stand for ?
7	Some examples to test the results accuracy.
8	Technical info

1. Getting started

Welcome to The Arbregen Software.
This is how the main form will look after loading a tree and running the software.
The file Sexe R Probable.arbre will be used as an example. Youll find this tree along with some other examples in the Arbregen directory.

1.1. How are the odds computed by the software ?
No premises are added about genotypes, beyond the ones built into the pedigree when designed by the user.
Those include phenotypes, genders, and assumptions about individuals at the borders of the tree (for example the probability for the root parents to be heterozygous). The software starts by giving a genotype to the root parents. It does this randomly, and according to the chosen a priori odds. It then mimics the meioses by picking an allele from each parent to provide each child with a genotype. If any incompatibility appears between the elected genotype and the actual phenotype built in the tree, the whole tree is discarded (for example, if one of the parents receives a homozygous normal genotype and one of their children shows the recessive phenotype). Only the trees which are fully data compatible will make it through.

Sorting out the odds of each genotype for each individual is easy at this point.
For instance 10000 trees have been computed, and 1000 appear not to be self contradictory. If 600 trees show the II-2 individual as being heterozygous and the other 400 as homozygous, then the odds for that individual to be heterozygous are 6 to 4 (i.e. a 60%probability).

The whole process is iterated, using different transmission modes (the software allows the user to restrict the computation to one or several particular modes).

If several modes appear to be consistent with the data (i.e. at least one tree passing through the sieve) an index of probability is given to compare the different modes. This index gives a clue to how likely each mode is to be the right one, but is not an actual probability.

1.2. Conventions

The software may handle only one character.
One character is determined by one gene with a pair of alleles
Normal allelic forms appear as n (if recessive) or N (if dominant).
Mutated allele abnormal forms appear as a (recessive) or A (dominant).

All possible combinations are listed below.

	Autosomal
	Homozygous normal	Heterozygous	Homozygous abnormal
Recessive mode	(N//N)	(N//a)	(a//a)
Dominant mode	(n//n)	(n//A)	(A//A)
	Sex linked
	Homozygous normal	Heterozygous	Homozygous abnormal
Recessive mode
Female	(N//N)	(N//a)	(a//a)
Male	(N//Y)		(a//Y)
Dominant mode
Female	(n//n)	(n//A)	(A//A)
Male	(n//Y)		(A//Y)