Summary: Here we report on an R package for genome-wide association studies of orthologous genes in bacteria. Before using the software, orthologs from bacterial genomes or metagenomes are defined using local or online implementations of OrthoMCL. These presence-absence patterns are statistically associated with variation in user-collected phenotypes using the Mono-Associated GNotobiotic Animals Metagenome-Wide Association R package (MAGNAMWAR). Genotype-phenotype associations can be performed with several different statistical tests based on the type and distribution of the data. Availability and implementation: MAGNAMWAR is available on CRAN. Contact: [email protected].

SUMMARY: BuchneraBASE is a bioinformatic research tool for the genome of the symbiotic bacterium Buchnera sp. APS that includes an improved genome annotation, comparative information about related insect symbiont genomes and a complete mapping of metabolic reactions to an Escherichia coli in silico model. The database is designed to accommodate genome-wide post-genomic datasets that are becoming available for this organism. AVAILABILITY: BuchneraBASE is available at http://www.buchnera.org/.