Send to

Choose Destination
Bioinformatics. 2019 Feb 15;35(4):546-552. doi: 10.1093/bioinformatics/bty669.

JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm.

Author information

Department of Biology, Brigham Young University, Provo, UT, USA.



Orthologous gene identification is fundamental to all aspects of biology. For example, ortholog identification between species can provide functional insights for genes of unknown function and is a necessary step in phylogenetic inference. Currently, most ortholog identification algorithms require all-versus-all BLAST comparisons, which are time-consuming and memory intensive.


In contrast to existing approaches, JustOrthologs exploits the conservation of gene structure by using the lengths of coding sequence regions and dinucleotide percentages to identify orthologs. In comparison to OrthoMCL, OMA and OrthoFinder, JustOrthologs decreases ortholog identification runtime by more than 96% and achieves comparable precision and recall scores. The computational speedup allowed us to conduct pairwise comparisons of 1197 complete genomes (780 eukaryotes and 417 archaea). We confirmed gene annotations for 384 120 genes, grouped 1 675 415 genes in previously unreported ortholog groups, and identified 51 429 potentially mislabeled genes across 622 843 ortholog groups.


JustOrthologs is an open source collaborative software package available in the GitHub repository: All test FASTA files used for comparisons are freely available at Reference genomes used in this work are available for download from the NCBI repository:


Supplementary data are available at Bioinformatics online.

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center