Format of input data

The format of data is shown in file BCMark1.txt, Linkage.txt, dhmark1.txt, dhmark2.txt, F2Marker.txt, LinkageZW.txt, MarkDH.txt in the Sample folder.

The first two columns in the above data file represent individual or sample ID, and sex code 0 for no sex; 1 for the hetergametic (ZW or XY); 2 for the homogametic (ZZ or XX). For the first column, the maximum value is the number of individuals. From the third column, each one identifies a molecular marker, and the number is determined by the molecular markers and matting types:1 for P1; 2 for P2 ; 3 for F1; 4 for BC1(F1×P1); 5 for BC2(F1×P2). Missing data is denoted by dot (".") or any positive integer beyond 1~5. It will be better to use 1 as the first genotype code. If other values are used, there are some misreading problems. If you know some markers are located on a same chromosome; however they are located into different linkage groups with a small cutoff criterion. You may do as follows,(1) Extract the data and save as a different file; (2) Set a larger cutoff criterion 100 cM or larger until they are grouped into together.

This model is developed by Jixiang Wu.

 

This is Coefficient-setting Box of Link Map, which will pop out automatically when you selected Link Map menu.

　

1.    Population Type

There are 4 kind of population accepted here, F2, BC, DH and RI population.

2.    Crossover Type

For some variety, such as silkworm, their crossover is different from average varieties. Crossover type provide 2 kind of Crossover type for a certain variety.

3.    Criterion Type

There are two kinds of Criteration Type here for building linkage group, Probability level and Morgan distance. 

4.    P value

If Criterion Type is Probability level, P value option is available. There are four significant level provided here, 0.05, 0.025, 0.01, 0.005.

5.    Morgan Distance(M)

If Criterion Type is Morgan Distance, Morgan Distance option is available. The Morgan Distance ranges from 0~1(M).

6.    Linkage Rule

There are 8 Linkage Rules listed here, single linkage, complete linkage, median linkage, centroid linkage, unweighted pair-group average, weighted pair-group average, flexable-beta method, and ward's method.

7.    Run

Run the data with selected model and model.

8.    Cancel

Leave the Coefficient-setting Box, and do nothing.

 

 

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