| 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 |
| 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 |
| Mpneumoniae | Data sets for the _Mycoplasma pneumoniae_ casestudy |
| 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 |
| 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 | Plot and summary of 'Binomix' objects |
| plot.Panmat | Plot and summary of 'Panmat' objects |
| plot.Panpca | Plot and summary of 'Panpca' objects |
| plot.Pantree | Plot and summary of 'Pantree' objects |
| plot.Rarefac | Plot and summary of '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 |
| readHmmer | Reading results from a HMMER3 scan |
| summary.Binomix | Plot and summary of 'Binomix' objects |
| summary.Panmat | Plot and summary of 'Panmat' objects |
| summary.Panpca | Plot and summary of 'Panpca' objects |
| summary.Pantree | Plot and summary of 'Pantree' objects |
| summary.Rarefac | Plot and summary of 'Rarefac' objects |
| xzcompress | Compressing and uncompressing text files |
| xzuncompress | Compressing and uncompressing text files |