# Microbial Pan-Genome Analysis

## Documentation for package ‘micropan’ version 2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

micropan-package | Microbial Pan-Genome Analysis
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
readBlastPair | Reads BLAST result files
readBlastSelf | Reads BLAST result files
readHmmer | Reading results from a HMMER3 scan
xmpl | Data sets for use in examples
xmpl.bclst | Data sets for use in examples
xmpl.bdist | Data sets for use in examples
xmpl.panmat | Data sets for use in examples
xzcompress | Compressing and uncompressing text files
xzuncompress | Compressing and uncompressing text files