Man pages for micropan
Microbial Pan-Genome Analysis

barrnapFinding rRNA genes
bClustClustering sequences based on pairwise distances
bDistComputes distances between sequences based on BLAST results
binomixEstimateBinomial mixture model estimates
blastAllAllMaking BLAST search all against all genomes
chaoThe Chao lower bound estimate of pan-genome size
dClustClustering sequences based on domain sequence
distJaccardComputing Jaccard distances between genomes
distManhattanComputing Manhattan distances between genomes
entrezDownloadDownloading genome data
findOrfsFinding ORFs in genomes
fluidityComputing genomic fluidity for a pan-genome
generic.BinomixPlot and summary of 'Binomix' objects
generic.PanmatPlot and summary of 'Panmat' objects
generic.PanpcaPlot and summary of 'Panpca' objects
generic.PantreePlot and summary of 'Pantree' objects
generic.RarefacPlot and summary of 'Rarefac' objects
geneWeightsGene cluster weighting
getAccessionsCollecting contig accession numbers
gff2fastaRetrieving sequences from genome
gffSignatureGFF signature text
heapsHeaps law estimate
hmmerCleanOverlapRemoving overlapping hits from HMMER3 scans
hmmerScanScanning a profile Hidden Markov Model database
isOrthologIdentifies orthologs in gene clusters
lorfsLongest ORF
micropanMicrobial Pan-Genome Analysis
mpneumoniaeData sets for the _Mycoplasma pneumoniae_ casestudy
orfLengthORF lengths
panMatrixComputing the pan-matrix for a set of gene clusters
panpcaPrincipal component analysis of a pan-matrix
panPrepPreparing FASTA files for pan-genomics
panTreeConstructing pan-genome trees
prodigalGene predictions using Prodigal
rarefactionRarefaction curves for a pan-genome
readBlastTableReading BLAST result file
readGFFReading and writing GFF-tables
readHmmerReading results from a HMMER3 scan
scores.loadingsPlotting scores and loadings in a 'Panpca' object
xzCompressing and uncompressing text files
micropan documentation built on Feb. 15, 2018, 5 p.m.