Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.
| Version: | 0.11 |
| Depends: | R (≥ 2.6.0), ape (≥ 2.4), adegenet |
| Imports: | graphics, utils |
| Suggests: | rgl |
| Published: | 2018-07-09 |
| Author: | Emmanuel Paradis [aut, cre, cph], Thibaut Jombart [aut, cph], Knaus Brian [aut, cph], Klaus Schliep [aut, cph], Alastair Potts [aut, cph], David Winter [aut, cph], Zhian N. Kamvar [aut, cph] |
| Maintainer: | Emmanuel Paradis <Emmanuel.Paradis at ird.fr> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | http://ape-package.ird.fr/pegas.html |
| NeedsCompilation: | yes |
| Citation: | pegas citation info |
| Materials: | NEWS |
| In views: | Phylogenetics |
| CRAN checks: | pegas results |
| Reference manual: | pegas.pdf |
| Vignettes: |
Reading Files |
| Package source: | pegas_0.11.tar.gz |
| Windows binaries: | r-devel: pegas_0.11.zip, r-release: pegas_0.11.zip, r-oldrel: pegas_0.11.zip |
| OS X binaries: | r-release: pegas_0.11.tgz, r-oldrel: pegas_0.11.tgz |
| Old sources: | pegas archive |
| Reverse depends: | adhoc, StAMPP |
| Reverse imports: | dartR, haplotypes, HierDpart, mmod, PopGenReport, poppr, rmetasim, skeleSim, spider, strataG |
| Reverse suggests: | adegenet, BarcodingR, hierfstat |
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