Directions for TYPSimSelector:
Select a dataset, a line of interest from those provided, and a sorting order.
Download raw data here.
(Unzipped file is ~6 GB)
Download raw data key here.
What is TYPSimSelector?
The TYPSimSelector sorts identity by state (IBS) values derived from SNP datasets
using PLINK v1.07 for accessions in the Ames Diversity Panel
(ADP; a USDA-maintained set of maize lines representing wide genetic variation in Ames, Iowa;
Romay et al., 2013).
The tool available here was conceived and implemented originally by Mark Millard at
the North Central Regional Plant Introduction Station (NCRPIS) to enable the use
of genomic similarity for germplasm management. Recognizing that this sort of
analysis would be useful for others as well, a collaboration to deploy the
mechanism via MaizeGDB was initiated in 2013.
This tool was developed by Emily Mauch with guidance from Carson Andorf,
Mark Millard, Cinta Romay, Ed Buckler, Candy Gardner, and Carolyn Lawrence.
As described by Romay et al., the ADP is a
set of approximately 2,500 maize accessions primarily made available via the NCRPIS in Ames, IA.
The panel was interrogated using over 680,000 SNP markers to establish identity by state (IBS) relationships.
This has proven useful for examining relationships between lines based upon similarity and divergence scores
(where identical lines are assigned a similarity score of 1 and a divergence is measured as 1-similarity).
How Similarity Scores were Calculated
Similarity scores were calculated as described by Romay, MC et al. 2013
Identity by state (IBS) was calculated for all possible pairwise
comparisons using PLINK v1.07
(Purcell et al., 2007).
Cite This Tool
If you are using the TYPSimSelector for your research then please cite MaizeGDB and Romay et. al. as follows: