Package: polysat
Version: 1.3-1
Date: 2012-10-14
Title: Tools for Polyploid Microsatellite Analysis
Author: Lindsay V. Clark <lvclark@illinois.edu>
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Depends: combinat, methods
Suggests: ade4, adegenet
Description: polysat is a collection of tools to handle microsatellite
data of any ploidy (and samples of mixed ploidy) where allele
copy number is not known in partially heterozygous genotypes.
It can import and export data in ABI GeneMapper, Structure,
ATetra, Tetrasat/Tetra, GenoDive, SPAGeDi, POPDIST, STRand, and
binary presence/absence formats.  It can calculate pairwise
distances between individuals using a stepwise mutation model
or infinite alleles model, with or without taking ploidies and
allele frequencies into account.  These distances can be used
for the calculation of clonal diversity statistics or used for
further analysis in R.  Allelic diversity statistics are also
available.  polysat can assist the user in estimating the
ploidy of samples, and lastly it can estimate allele
frequencies in populations, calculate pairwise Fst values based
on those frequencies, and export allele frequencies to SPAGeDi
and adegenet.
License: GPL (>= 2)
URL: http://openwetware.org/wiki/Polysat
Packaged: 2012-10-16 00:45:18 UTC; lvclark
Repository: CRAN
Date/Publication: 2012-10-16 05:17:43

Package: polysat
Version: 1.3-2
Date: 2013-09-03
Title: Tools for Polyploid Microsatellite Analysis
Author: Lindsay V. Clark <lvclark@illinois.edu>
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Depends: combinat, methods
Suggests: ade4, adegenet
Description: polysat is a collection of tools to handle microsatellite data of
any ploidy (and samples of mixed ploidy) where allele copy number is not
known in partially heterozygous genotypes.  It can import and export data in
ABI GeneMapper, Structure, ATetra, Tetrasat/Tetra, GenoDive, SPAGeDi,
POPDIST, STRand, and binary presence/absence formats.  It can calculate
pairwise distances between individuals using a stepwise mutation model or
infinite alleles model, with or without taking ploidies and allele frequencies
into account.  These distances can be used for the calculation of clonal
diversity statistics or used for further analysis in R.  Allelic diversity
statistics are also available.  polysat can assist the user in estimating the
ploidy of samples, and lastly it can estimate allele frequencies in
populations, calculate pairwise Fst values based on those frequencies, and
export allele frequencies to SPAGeDi and adegenet.
License: GPL-2
URL: http://openwetware.org/wiki/Polysat
Packaged: 2013-09-06 02:17:53 UTC; lvclark
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-09-06 06:36:43