Gcluster: a simple-to-use tool for visualizing and comparing genome contexts for numerous genomes
Xiangyang Li, Fang Chen, Yunpeng Chen
Abstract
MOTIVATION: Comparing the organization of gene, gene clusters and their flanking genomic contexts is of critical importance to the determination of gene function and evolutionary basis of microbial traits. Currently, user-friendly and flexible tools enabling to visualize and compare genomic contexts for numerous genomes are still missing. RESULTS: We here present Gcluster, a stand-alone Perl tool that allows researchers to customize and create high-quality linear maps of the genomic region around the genes of interest across large numbers of completed and draft genomes. Importantly, Gcluster integrates homologous gene analysis, in the form of a built-in orthoMCL, and mapping genomes onto a given phylogeny to provide superior comparison of gene contexts. AVAILABILITY AND IMPLEMENTATION: Gcluster is written in Perl and released under GPLv3. The source code is freely available at https://github.com/Xiangyang1984/Gcluster and http://www.microbialgenomic.com/Gcluster_tool.html. Gcluster can also be installed through conda: 'conda install -c bioconda gcluster'. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.