Microbial Pan-Genome Analysis
Clustering sequences based on pairwise distances
Computes distances between sequences
Binomial mixture model estimates
Making BLAST search all against all genomes
The Chao lower bound estimate of pan-genome size
Clustering sequences based on domain sequence
Computing Jaccard distances between genomes
Computing Manhattan distances between genomes
Downloading genome data
Computing genomic fluidity for a pan-genome
Gene cluster weighting
Collecting contig accession numbers
Heaps law estimate
Removing overlapping hits from HMMER3 scans
Scanning a profile Hidden Markov Model database
Identifies orthologs in gene clusters
Microbial Pan-Genome Analysis
Computing the pan-matrix for a set of gene clusters
Principal component analysis of a pan-matrix
Preparing FASTA files for pan-genomics
Rarefaction curves for a pan-genome
Reads BLAST result files
Reading results from a HMMER3 scan
Data sets for use in examples
Compressing and uncompressing text files
A collection of functions for computations and visualizations of microbial pan-genomes.