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In the new release you can use in some functions parallel working. The functions are codeGeno, pairwiseLD, ...
a new release of synbreed is now on CRAN. Functions write.vcf, read.vcf2matrix and read.vcf2list are added. Further beagle 4.0 with its source is included. gzip is not needed any more as external tool.
A new version of synbreed is now available on CRAN. Due to the policies of R we removed the beagle.jar file from the package. If you like to use the beagle option for imputing, the explanation of how to use it is provided in the manual of the codeGeno-function. Get the package from http://cran.r-project.org/web/packages/synbreed/