Genome Identifier: A Tool for Phylogenetic Analysis of Microbial Genomes

Abstract

: Bacterial whole-genome sequences have recently become widely available via innovative and rapid progress in technologies such as high-throughput sequencing and computing. Genomes of environmental microor-ganisms have also been sequenced, and their number is expected to increase in the future. Typically, phylogenetic analysis is performed after genome sequencing of such organisms. 16S rRNA is a standard locus for the phylogenetic analysis of prokaryotes. However, 16S rRNA phylogenetic trees are not always reliable because of out-paralogs and horizontal gene transfer. To overcome this problem, multiple genes (or proteins) should be employed. Therefore, we developed “Genome Identifier,” which can be used for constructing a concatenated phylogenetic tree in the form of a species tree by predicting genes from newly sequenced genomic data and collecting homologous sequences from other species.