{"entity": "publication", "iuid": "5c99b2c1a294412499cdd96f6f69f96d", "timestamp": "2026-03-17T00:41:30.122Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5c99b2c1a294412499cdd96f6f69f96d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5c99b2c1a294412499cdd96f6f69f96d"}}, "title": "Improved orthology inference with Hieranoid 2.", "authors": [{"family": "Kaduk", "given": "Mateusz", "initials": "M"}, {"family": "Sonnhammer", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2017-04-15", "journal": {"title": "Bioinformatics", "issn": "1367-4803", "volume": "33", "issue": "8", "pages": "1154-1159", "issn-l": null}, "abstract": "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.\n\nWe 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.\n\nmateusz.kaduk@scilifelab.se.\n\nPerl code freely available at http://hieranoid.sbc.su.se/ .\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btw774", "pmid": "28096085", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "btw774"}], "notes": [], "created": "2018-12-05T12:31:02.616Z", "modified": "2018-12-05T12:31:02.638Z"}