Bacillus-Genomes

• a collection of programs written for Bacillus Genome projects
• detailed instructions for running the programs can be found in README.md of each folder

Bootstrapped Ecotype

• calculates a bootstrapped score for each demarcated ecotype based on rarefaction results
• adds ecotype bootstrap score to the phylogenetic tree
• plots the phylogenetic tree with bootstrapped scores and ecotype annotation

Clone Identification

• Identifies all possible clone strains in a core genome alignment file

Compute ER

• Computes pairwise sequence divergence of all strains in the input fasta file

Gene Divergence

• Computes average pairwise gene divergence/gene divergence percentage of all strains for a single gene
• Summarize single gene rarefaction results
• Plot a graph of the relationship between gene average divergence/gene divergence percentage and ecotype size for each species

Gene Extractor

• creates sql databases to store information of genes for each species
• extract all genes of the given species
• extract all core genes in a given core genome alignment file

Gene Length

• a small program that graphs the distribution of gene length in each species

Random Gene Generator

• generates random fake gene/real gene samples for rarefaction analysis. All sample with replacement
• generate single gene samples of all genes in a given species

Rarefaction Analysis

analyzes and plot graphs of rarefaction results

Rename

matches the new ecotype demarcations with past ecotype demarcations (kept as backup in case we need it in the future)

Util

util folder that contains utility functions used in other programs