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 microorganisms 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.