bClust                  Clustering sequences based on pairwise
                        distances
bDist                   Computes distances between sequences
binomixEstimate         Binomial mixture model estimates
blastpAllAll            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
micropan                Microbial Pan-Genome Analysis
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
rarefaction             Rarefaction curves for a pan-genome
readBlastSelf           Reads BLAST result files
readHmmer               Reading results from a HMMER3 scan
xmpl                    Data sets for use in examples
xzcompress              Compressing and uncompressing text files
