• Genomic Mating
  • Simulation

Step 1:Data input

Users can upload ped, map, and phe files for the analysis. Birthyear, Estimated Breeding Values (EBV), and sex information for each individual may be defined in a sample information txt file. Please --download the example datasets-- and check the tutorial for detailed information about the file formats. The PED, MAP, phenotype, and sample information files should be named with the suffix of “.ped”, “.map”, ”.phe”, and “.txt”, respectively. Please note, users can upload a file with a maximum size of 50MB. Datasets larger than that should be uploaded via FTP or analyzed locally with the  standalone package.

Please upload the .ped file:

or select an uploaded file

or use an example dataset




Please upload the .map file:

or select an uploaded file

or use an example dataset




Please upload the .phe file:

or select an uploaded file

or use an example dataset



When EBVs are available in sample information, users can skip uploading phe file




Please upload the sample_infomation.txt file:

or select an uploaded file

or use an example dataset




Step 2: Marker filtration

High levels of linkage disequilibrium (LD) and low quality SNPs affect both performance and efficiency of GM. High LD and low quality SNPs were pruned by default. Please note, analysis of large dataset could be very slow when turning off this setting.

LD pruning and quality control 

Step 3: Submit your job

Be notifled by email (Tick this box if you want to be notified by email when the results are available)




if available,the title will be included in the subject of the notification email and can be used as a way to identify your analysis.

Results

You may bookmark the following web address and view your results later. Please note that the results will be stored for 7 days.


Your job is currently running ... Please be patient. Analysis successful ! The analysis is failed. Please verify the formats of your input files. In case that you are using the example datasets from FigShare (Version 1) , please note that the error is caused by a wrong sample_information file. We have updated this file in the lastest version of the examples (https://figshare.com/articles/dataset/AMBP_case_study/19390652).


Mate allocation strategy and optimum numbers of offspring for each pair.





Mate allocation for each candidates.



Download all the results