Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences. - Alexander F. Auch; Stefan R. Henz; Barbara R. Holland; Markus Göker (BMC Bioinform., 2006)

COPYCAT : cophylogenetic analysis tool. - Jan P. Meier-Kolthoff; Alexander F. Auch; Daniel H. Huson; Markus Göker (Bioinform., 2007)

AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa. - Alexandros Stamatakis; Alexander F. Auch; Jan P. Meier-Kolthoff; Markus Göker (BMC Bioinform., 2007)

Large-Scale Co-Phylogenetic Analysis on the Grid. - Heinz Stockinger; Alexander F. Auch; Markus Göker; Jan P. Meier-Kolthoff; Alexandros Stamatakis (Int. J. Grid High Perform. Comput., 2009)

opm: an R package for analysing OmniLog® phenotype microarray data. - Lea A. I. Vaas; Johannes Sikorski; Benjamin Hofner; Anne Fiebig; Nora Buddruhs; Hans-Peter Klenk; Markus Göker (Bioinform., 2013)

Genome sequence-based species delimitation with confidence intervals and improved distance functions. - Jan P. Meier-Kolthoff; Alexander F. Auch; Hans-Peter Klenk; Markus Göker (BMC Bioinform., 2013)

Highly parallelized inference of large genome-based phylogenies. - Jan P. Meier-Kolthoff; Alexander F. Auch; Hans-Peter Klenk; Markus Göker (Concurr. Comput. Pract. Exp., 2014)

Controlling false discoveries in high-dimensional situations: boosting with stability selection. - Benjamin Hofner; Luigi Boccuto; Markus Göker (BMC Bioinform., 2015)

Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets. - Aitor Blanco-Míguez; Jan P. Meier-Kolthoff; Alberto Gutiérrez-Jácome; Markus Göker; Florentino Fdez-Riverola; Borja Sánchez; Anália Lourenço (PLoS Comput. Biol., 2016)

VICTOR: genome-based phylogeny and classification of prokaryotic viruses. - Jan P. Meier-Kolthoff; Markus Göker (Bioinform., 2017)

TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. - Jan P. Meier-Kolthoff; Joaquim Sardà Carbasse; Rosa L. Peinado-Olarte; Markus Göker (Nucleic Acids Res., 2022)