Man pages for micropan
Microbial Pan-Genome Analysis

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
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
heapsHeaps law estimate
hmmerCleanOverlapRemoving overlapping hits from HMMER3 scans
hmmerScanScanning a profile Hidden Markov Model database
isOrthologIdentifies orthologs in gene clusters
mpneumoniaeData sets for the _Mycoplasma pneumoniae_ casestudy
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
prodigalPredictGene predictions using Prodigal
rarefactionRarefaction curves for a pan-genome
readBlastTableReading BLAST result file
readHmmerReading results from a HMMER3 scan
scores.loadingsPlotting scores and loadings in a 'Panpca' object
xzCompressing and uncompressing text files
micropan documentation built on May 29, 2017, 11:57 a.m.