Can SNPAnalyzer tool can analyse bovine SNP data. If not can anyone suggest any software for haplotype estimation and LD calculation from unphased genotypic data (bovine)
Yes PROVEAN database that is available through this link; http://provean.jcvi.org/index.php, may answer your questions in respect of evaluating non-human SNP data. for LD from haplotypic data you may use Arlequin software from this link; http://cmpg.unibe.ch/software/arlequin35/, and /or Haploview, https://www.broadinstitute.org/haploview/browsing-linkage-disequilibrium....