├── DESCRIPTION ├── NAMESPACE ├── R ├── bclust.R ├── bdist.R ├── binomix.R ├── blasting.R ├── domainclust.R ├── entrez.R ├── extern.R ├── extractPanGenes.R ├── genomedistances.R ├── hmmer3.R ├── micropan.R ├── panmat.R ├── panpca.R ├── panprep.R ├── powerlaw.R ├── rarefaction.R ├── xmpl.R └── xz.R ├── Readme.Rmd ├── Readme.md ├── Readme_files ├── figure-gfm │ ├── unnamed-chunk-10-1.png │ ├── unnamed-chunk-15-1.png │ ├── unnamed-chunk-16-1.png │ ├── unnamed-chunk-20-1.png │ ├── unnamed-chunk-21-1.png │ ├── unnamed-chunk-26-1.png │ ├── unnamed-chunk-27-1.png │ ├── unnamed-chunk-28-1.png │ ├── unnamed-chunk-29-1.png │ ├── unnamed-chunk-30-1.png │ ├── unnamed-chunk-31-1.png │ ├── unnamed-chunk-32-1.png │ ├── unnamed-chunk-8-1.png │ └── unnamed-chunk-9-1.png └── figure-markdown_github │ ├── unnamed-chunk-10-1.png │ ├── unnamed-chunk-14-1.png │ ├── unnamed-chunk-16-1.png │ ├── unnamed-chunk-18-1.png │ ├── unnamed-chunk-20-1.png │ ├── unnamed-chunk-21-1.png │ ├── unnamed-chunk-25-1.png │ ├── unnamed-chunk-26-1.png │ ├── unnamed-chunk-27-1.png │ ├── unnamed-chunk-28-1.png │ ├── unnamed-chunk-29-1.png │ ├── unnamed-chunk-30-1.png │ ├── unnamed-chunk-31-1.png │ ├── unnamed-chunk-32-1.png │ ├── unnamed-chunk-7-1.png │ ├── unnamed-chunk-8-1.png │ └── unnamed-chunk-9-1.png ├── data ├── xmpl.bclst.rda ├── xmpl.bdist.rda └── xmpl.panmat.rda ├── inst └── extdata │ ├── GID1_vs_GID1_.txt.xz │ ├── GID1_vs_microfam.hmm.txt.xz │ ├── GID2_vs_GID1_.txt.xz │ ├── GID2_vs_GID2_.txt.xz │ ├── GID2_vs_microfam.hmm.txt.xz │ ├── GID3_vs_GID1_.txt.xz │ ├── GID3_vs_GID2_.txt.xz │ ├── GID3_vs_GID3_.txt.xz │ ├── GID3_vs_microfam.hmm.txt.xz │ ├── microfam.hmm.h3f.xz │ ├── microfam.hmm.h3i.xz │ ├── microfam.hmm.h3m.xz │ ├── microfam.hmm.h3p.xz │ ├── xmpl.faa.xz │ ├── xmpl_GID1.faa.xz │ ├── xmpl_GID2.faa.xz │ └── xmpl_GID3.faa.xz ├── man ├── bClust.Rd ├── bDist.Rd ├── binomixEstimate.Rd ├── blastpAllAll.Rd ├── chao.Rd ├── dClust.Rd ├── distJaccard.Rd ├── distManhattan.Rd ├── entrezDownload.Rd ├── 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