bClust                  Clustering sequences based on pairwise
                        distances
bDist                   Computes distances between sequences based on
                        BLAST results
barrnap                 Finding rRNA genes
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
findOrfs                Finding ORFs in genomes
fluidity                Computing genomic fluidity for a pan-genome
geneWeights             Gene cluster weighting
getAccessions           Collecting contig accession numbers
gff2fasta               Retrieving sequences from genome
gffSignature            GFF signature text
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
lorfs                   Longest ORF
micropan                Microbial Pan-Genome Analysis
mpneumoniae             Data sets for the _Mycoplasma pneumoniae_
                        casestudy
orfLength               ORF lengths
panMatrix               Computing the pan-matrix for a set of gene
                        clusters
panPrep                 Preparing FASTA files for pan-genomics
panTree                 Constructing pan-genome trees
panpca                  Principal component analysis of a pan-matrix
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
plotScores              Plotting scores and loadings in a 'Panpca'
                        object
prodigal                Gene predictions using Prodigal
rarefaction             Rarefaction curves for a pan-genome
readBlastTable          Reading BLAST result file
readGFF                 Reading and writing GFF-tables
readHmmer               Reading results from a HMMER3 scan
xzcompress              Compressing and uncompressing text files
