Does anybody know how to prepare the input file for similarity matrices in NTSYS for SNP data while we have heterozygous individuals?
SM works on 1,0,0.5 data but Jaccard not? Should the scoring be 1,0,-1 or 0,1,2 or any suggestions?
interesting question. I recently attended a training and this was mentioned. let me go through my notes and exercises and will return to you
I have the same problem. does anybody how to score SNP data to perform similarity analysis in NTSYS based on Dice?
I have the same question. If someone find the answer, let me know, please!
First of all you have to score your gels into binary format i.e. 1/0 ( 1 for presence and 0 for absence of allele) and then prepare your input file as below;
1. In excel sheet Cell 1A write 1 (rectangular) then Cell 1B- No of Markers (in rows) (Count allele as marker) , Cell 1C- No of genotypes (in column) and cell 1D- symbol use for missing value.
2. You can also check whether your input file is correct or not in NTSys software before your process to analysis.
3. You will find more information in help menu.
Best of luck for your analysis.
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