micropan

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