A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database

The PhIGs database currently contains 23 completely sequenced genomes of fungi and metazoans, containing 409,653 genes that have been grouped into 42,645 gene clusters. Each gene cluster is built such that the gene sequence distances are consistent with the known organismal relationships and in so doing, maximizing the likelihood for the clusters to represent truly orthologous genes. The PhIGs website contains tools that allow the study of genes within their phylogenetic framework through keyword searches on annotations, such as GO and InterPro assignments, and sequence similarity searches by BLAST and HMM. In addition to displaying the evolutionary relationships of the genes in each cluster, the website also allows users to view the relative physical positions of homologous genes in specified sets of genomes.Accurate analyses of genes and genomes can only be done within their full phylogenetic context. The PhIGs database and corresponding website http://phigs.org webcite address this problem for the scientific community. Our goal is to expand the content as more genomes are sequenced and use this framework to incorporate more analyses.The continually increasing number of whole genome sequencing projects has underscored the need for a high-throughput methodology to sort genes into orthologous sets to facilitate genome analysis. With a more robust understanding of the evolutionary history for each gene in the genome, not only can we more accurately transfer annotation across organisms, but we can also address larger biological questions regarding the evolution of genomes and species as well as the functional and biochemical processes encoded within each genome. Currently, most gene annotations rely on homologs identified by pair-wise sequence similarity to transfer the presumed function. This approach has been shown to have many drawbacks [1] which lead to annotation errors. Incorrect assignments are generally due to gene duplication events [2] giving rise to paralog