Dear all,
A new version of pegas is under preparation. It includes several new
functions for LD mapping, a new na.omit function to check for missing
alleles, improved code for VCF files and for extracting haplotypes from
"loci" objects. The list of these new features can be found on GitHub:
https://github.com/emmanuelparadis/pegas/blob/master/pegas/NEWS
A testing version is available (0.8-2.7) from GitHub and from ape's site
where a Windows version is also available:
http://ape-package.ird.fr/ape_installation.html#versions
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