Mpneumoniae             Data sets for the _Mycoplasma pneumoniae_
                        casestudy
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-package        Microbial Pan-genome Analysis
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            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
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
translate               From nucleotides to proteins
xzcompress              xz (un)compress a file
