| micropan-package | Microbial Pan-genome Analysis |
| bClust | Clustering sequences based on pairwise distances |
| bDist | Computes distances between sequences based on BLAST results |
| binomixEstimate | Binomial mixture model estimates |
| blastAllAll | Making BLAST search all against all genomes |
| chao | The Chao lower bound estimate of pan-genome size |
| dClust | Clustering sequences based on domain sequence |
| distJaccard | Computing Jaccard distances between genomes |
| distManhattan | Computing Manhattan distances between genomes |
| entrezDownload | Downloading genome data |
| fluidity | Computing genomic fluidity for a pan-genome |
| geneWeights | Gene cluster weighting |
| getAccessions | Collecting contig accession numbers |
| gregexpr | Extended 'gregexpr' with substring retrieval |
| heaps | Heaps law estimate |
| hmmerCleanOverlap | Removing overlapping hits from HMMER3 scans |
| hmmerScan | Scanning a profile Hidden Markov Model database |
| isOrtholog | Identifies orthologs in gene clusters |
| micropan | Microbial Pan-genome Analysis |
| Mpneumoniae | Data sets for the _Mycoplasma pneumoniae_ casestudy |
| Mpneumoniae.blast.clustering | Data sets for the _Mycoplasma pneumoniae_ casestudy |
| Mpneumoniae.blast.distances | Data sets for the _Mycoplasma pneumoniae_ casestudy |
| Mpneumoniae.blast.panmat | Data sets for the _Mycoplasma pneumoniae_ casestudy |
| Mpneumoniae.domain.clustering | Data sets for the _Mycoplasma pneumoniae_ casestudy |
| Mpneumoniae.domain.panmat | Data sets for the _Mycoplasma pneumoniae_ casestudy |
| Mpneumoniae.table | Data sets for the _Mycoplasma pneumoniae_ casestudy |
| nonoverlap | Removing overlapping hits from HMMER3 scans |
| objectFun | Heaps law estimate |
| panColor | Plotting and printing 'Binomix' objects |
| panMatrix | Computing the pan-matrix for a set of gene clusters |
| panpca | Principal component analysis of a pan-matrix |
| panPrep | Preparing FASTA files for pan-genomics |
| panTree | Constructing pan-genome trees |
| plot.Binomix | Plotting and printing 'Binomix' objects |
| plot.Fasta | Plotting and printing 'Fasta' objects |
| plot.Panmat | Plotting and printing 'Panmat' objects |
| plot.Panpca | Plotting and printing 'Panpca' objects |
| plot.Pantree | Plotting and printing 'Pantree' objects |
| plot.Rarefac | Plotting and printing 'Rarefac' objects |
| plotLoadings | Plotting scores and loadings in a 'Panpca' object |
| plotScores | Plotting scores and loadings in a 'Panpca' object |
| prodigalPredict | Gene predictions using Prodigal |
| rarefaction | Rarefaction curves for a pan-genome |
| readBlastTable | Reading BLAST result file |
| readFasta | Read and write biological sequence files. |
| readHmmer | Reading results from a HMMER3 scan |
| reverseComplement | Reverse-complement of a DNA or RNA sequence |
| str.Binomix | Plotting and printing 'Binomix' objects |
| str.Fasta | Plotting and printing 'Fasta' objects |
| str.Panmat | Plotting and printing 'Panmat' objects |
| str.Panpca | Plotting and printing 'Panpca' objects |
| str.Pantree | Plotting and printing 'Pantree' objects |
| str.Rarefac | Plotting and printing 'Rarefac' objects |
| summary.Binomix | Plotting and printing 'Binomix' objects |
| summary.Fasta | Plotting and printing 'Fasta' objects |
| summary.Panmat | Plotting and printing 'Panmat' objects |
| summary.Panpca | Plotting and printing 'Panpca' objects |
| summary.Pantree | Plotting and printing 'Pantree' objects |
| summary.Rarefac | Plotting and printing 'Rarefac' objects |
| translate | From nucleotides to proteins |
| writeFasta | Read and write biological sequence files. |
| xzcompress | xz (un)compress a file |
| xzuncompress | xz (un)compress a file |