READ ME FILE

Overview:

Population determination is usually based upon geographical origin of samples or phenotypes but due to unidentified barriers to gene-flow they are not discretely distributed.

The software "Goaty Le" is based on population genetics for assigning breeds among 3 selected population and identifying immigrants.

The software mainly performs the task of demonstrating the presence of
population structure, assigning individuals to population and identifying migrants.

At back end it uses another software for carrying out the above task.
Software named "STRUCTURE 2.1" is used for calculating Fst values and finding Maximum Likelihood
for the population data. It mainly uses Bayesian approach to find Maximum Likelihood and Fst values which then forms a cluster of a population.

A model is assumed in which there are K population (K is probability of an individual to fall under any
one population), each of which is characterized by a set of allele frequencies at each locus(Marker).

It is assumed that the loci are at Hardy-Weinberg equilibrium within population .
This model assumes that markers are not in linkage disequilibrium (LD) within subpopulation so that one
can deal with weakly linked markers.Data here taken are from diploid organism.

Software used here does all the task by using the below methods:

1.Maximum Likelihood.

2.F-Statistics.

3.MCMC Algorithm.

4.Drichilet Distance.

5.Gamma Distribution.

Parameters for all this methods used in the software are set as default along with its data (dinucleotide OR trinucleotide).

To ensure sensible result some care is to be taken while entering data and running the
software.

About the Software:

The software package "Goaty Lè" merges two interface COMMAND LINE & FRONT END.
Structure is executed on command line and Data entering & Result interpretation is displayed on front-end.

"For accuracy in the result obtained by using this software , run your data with each population about 10-20 times, and the maximum value obtained(~=0.99 probability) gives the assigned breed for an individual."

Entering Data:

Data entering requires a proper experimentally derived result and proper know-how about all the range for a given marker, any random data are not acceptable and so is not recommended.

In an exceptional case without a prior knowledge of data and its range is designed where for testing purpose press"Load Data " which will enter default data in each field,this is mainly done for getting acquainted with the software (see sample data on the main page).

An outline of a data and its range are :
Individual should be a Diploid organism (2n), and for each loci (Marker position) its corresponding
AMPLICON FRAGMENT is measured .

Three main parameters (which are non-genotypic values) are to be taken into consideration:
1.Population ID (3 digit numeric value).
2.Population No(1,2,or 3 for Zalawadi,Gohilwadi,and Surti respectively).
3.Population Flag(0 or 1 for using population no in the data).

Genotypic values are entered into the text boxes given near each of the marker name.
Each value enetered is specific for an individual and locus.

Data entered within this range would give nearly accurate result and for missing data enter -9 for both the genotypes of a particular marker

Result:

Result page consists of maximum probable value for an individual to fall under a population.
First line shows all the values for each population, while next line shows highest probability
among them, and the last line shows highlighted population name.

The first line also indicates probable parentage and grand-parentage of an individual where highest probability indicates the population assigned to the individual.

The program will attempt to provide some indication about the nature of any problems that exist.

**For getting accurate result POP FlAG must be kept "1" every time you run the program.