Improved orthology inference with Hieranoid 2

Bioinformatics. 2017 Apr 15;33(8):1154-1159. doi: 10.1093/bioinformatics/btw774.


Motivation: The initial step in many orthology inference methods is the computationally demanding establishment of all pairwise protein similarities across all analysed proteomes. The quadratic scaling with proteomes has become a major bottleneck. A remedy is offered by the Hieranoid algorithm which reduces the complexity to linear by hierarchically aggregating ortholog groups from InParanoid along a species tree.

Results: We have further developed the Hieranoid algorithm in many ways. Major improvements have been made to the construction of multiple sequence alignments and consensus sequences. Hieranoid version 2 was evaluated with standard benchmarks that reveal a dramatic increase in the coverage/accuracy tradeoff over version 1, such that it now compares favourably with the best methods. The new parallelized cluster mode allows Hieranoid to be run on large data sets in a much shorter timespan than InParanoid, yet at similar accuracy.


Availability and implementation: Perl code freely available at .

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Algorithms*
  • Computational Biology / methods*
  • Sequence Alignment
  • Sequence Homology*
  • Software