Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets. - Luis Miguel Rodriguez-Rojas; Konstantinos T. Konstantinidis (Bioinform., 2014)

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. - Luis Miguel Rodriguez-Rojas; Santosh Gunturu; William T. Harvey; Ramon Rosselló-Mora; James M. Tiedje; James R. Cole; Konstantinos T. Konstantinidis (Nucleic Acids Res., 2018)

MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes. - Carlos A. Ruiz-Perez; Roth E. Conrad; Konstantinos T. Konstantinidis (BMC Bioinform., 2021)

RecruitPlotEasy: An Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity. - Kenji Gerhardt; Carlos A. Ruiz-Perez; Luis M. Rodriguez-R; Roth E. Conrad; Konstantinos T. Konstantinidis (Frontiers Bioinform., 2021)